diff --git a/src/calibre/ebooks/oeb/polish/container.py b/src/calibre/ebooks/oeb/polish/container.py
index 604c4c3c37..d6554cf015 100644
--- a/src/calibre/ebooks/oeb/polish/container.py
+++ b/src/calibre/ebooks/oeb/polish/container.py
@@ -95,6 +95,7 @@ class Container(object):  # {{{
 
     book_type = 'oeb'
     SUPPORTS_TITLEPAGES = True
+    SUPPORTS_FILENAMES = True
 
     def __init__(self, rootpath, opfpath, log, clone_data=None):
         self.root = clone_data['root'] if clone_data is not None else os.path.abspath(rootpath)
@@ -1035,6 +1036,7 @@ class AZW3Container(Container):
 
     book_type = 'azw3'
     SUPPORTS_TITLEPAGES = False
+    SUPPORTS_FILENAMES = False
 
     def __init__(self, pathtoazw3, log, clone_data=None, tdir=None):
         if clone_data is not None:
diff --git a/src/calibre/ebooks/oeb/polish/replace.py b/src/calibre/ebooks/oeb/polish/replace.py
index d6d3e14a19..77cc8c7073 100644
--- a/src/calibre/ebooks/oeb/polish/replace.py
+++ b/src/calibre/ebooks/oeb/polish/replace.py
@@ -7,7 +7,7 @@ __license__   = 'GPL v3'
 __copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
 __docformat__ = 'restructuredtext en'
 
-import codecs, shutil, os
+import codecs, shutil, os, posixpath
 from urlparse import urlparse
 from collections import Counter, defaultdict
 
@@ -146,25 +146,50 @@ def replace_file(container, name, path, basename, force_mt=None):
         with container.open(nname, 'wb') as dest:
             shutil.copyfileobj(src, dest)
 
-def get_recommended_folders(container, names):
-    ' Return the folders that are recommended for the given filenames '
+def mt_to_category(container, mt):
     from calibre.ebooks.oeb.polish.container import guess_type, OEB_FONTS
     from calibre.ebooks.oeb.base import OEB_DOCS, OEB_STYLES
-    counts = defaultdict(Counter)
-    def mt_to_category(mt):
-        if mt in OEB_DOCS:
-            category = 'text'
-        elif mt in OEB_STYLES:
-            category = 'style'
-        elif mt in OEB_FONTS:
-            category = 'font'
-        else:
-            category = mt.partition('/')[0]
-        return category
+    if mt in OEB_DOCS:
+        category = 'text'
+    elif mt in OEB_STYLES:
+        category = 'style'
+    elif mt in OEB_FONTS:
+        category = 'font'
+    elif mt == guess_type('a.opf'):
+        category = 'opf'
+    elif mt == guess_type('a.ncx'):
+        category = 'toc'
+    else:
+        category = mt.partition('/')[0]
+    return category
 
+def get_recommended_folders(container, names):
+    ' Return the folders that are recommended for the given filenames '
+    from calibre.ebooks.oeb.polish.container import guess_type
+    counts = defaultdict(Counter)
     for name, mt in container.mime_map.iteritems():
         folder = name.rpartition('/')[0] if '/' in name else ''
-        counts[mt_to_category(mt)][folder] += 1
+        counts[mt_to_category(container, mt)][folder] += 1
 
     recommendations = {category:counter.most_common(1)[0][0] for category, counter in counts.iteritems()}
-    return {n:recommendations.get(mt_to_category(guess_type(os.path.basename(n))), '') for n in names}
+    return {n:recommendations.get(mt_to_category(container, guess_type(os.path.basename(n))), '') for n in names}
+
+def rationalize_folders(container, folder_type_map):
+    all_names = set(container.mime_map)
+    new_names = set()
+    name_map = {}
+    for name in all_names:
+        category = mt_to_category(container, container.mime_map[name])
+        folder = folder_type_map.get(category, None)
+        if folder is not None:
+            bn = posixpath.basename(name)
+            new_name = posixpath.join(folder, bn)
+            if new_name != name:
+                c = 0
+                while new_name in all_names or new_name in new_names:
+                    c += 1
+                    n, ext = bn.rpartition('.')[0::2]
+                    new_name = posixpath.join(folder, '%s_%d.%s' % (n, c, ext))
+                name_map[name] = new_name
+                new_names.add(new_name)
+    return name_map
diff --git a/src/calibre/gui2/tweak_book/__init__.py b/src/calibre/gui2/tweak_book/__init__.py
index d38e56f91b..e4a6586c94 100644
--- a/src/calibre/gui2/tweak_book/__init__.py
+++ b/src/calibre/gui2/tweak_book/__init__.py
@@ -38,6 +38,7 @@ d['preview_mono_font_size'] = 14
 d['preview_minimum_font_size'] = 8
 d['remove_existing_links_when_linking_sheets'] = True
 d['charmap_favorites'] = list(map(ord, '\xa0\u2002\u2003\u2009\xad' '‘’“”‹›«»‚„' '—–§¶†‡©®™' '→⇒•·°±−×÷¼½½¾' '…µ¢£€¿¡¨´¸ˆ˜' 'ÀÁÂÃÄÅÆÇÈÉÊË' 'ÌÍÎÏÐÑÒÓÔÕÖØ' 'ŒŠÙÚÛÜÝŸÞßàá' 'âãäåæçèéêëìí' 'îïðñòóôõöøœš' 'ùúûüýÿþªºαΩ∞'))  # noqa
+d['folders_for_types'] = {'style':'styles', 'image':'images', 'font':'fonts', 'audio':'audio', 'video':'video'}
 
 del d
 
diff --git a/src/calibre/gui2/tweak_book/boss.py b/src/calibre/gui2/tweak_book/boss.py
index fd04f3cb62..9e310ac6ee 100644
--- a/src/calibre/gui2/tweak_book/boss.py
+++ b/src/calibre/gui2/tweak_book/boss.py
@@ -21,7 +21,7 @@ from calibre.ebooks.oeb.polish.main import SUPPORTED, tweak_polish
 from calibre.ebooks.oeb.polish.container import get_container as _gc, clone_container, guess_type, OEB_FONTS
 from calibre.ebooks.oeb.polish.cover import mark_as_cover, mark_as_titlepage
 from calibre.ebooks.oeb.polish.pretty import fix_all_html, pretty_all
-from calibre.ebooks.oeb.polish.replace import rename_files, replace_file, get_recommended_folders
+from calibre.ebooks.oeb.polish.replace import rename_files, replace_file, get_recommended_folders, rationalize_folders
 from calibre.ebooks.oeb.polish.split import split, merge, AbortError
 from calibre.ebooks.oeb.polish.toc import remove_names_from_toc, find_existing_toc
 from calibre.ebooks.oeb.polish.utils import link_stylesheets
@@ -36,6 +36,7 @@ from calibre.gui2.tweak_book.toc import TOCEditor
 from calibre.gui2.tweak_book.editor import editor_from_syntax, syntax_from_mime
 from calibre.gui2.tweak_book.editor.insert_resource import get_resource_data, NewBook
 from calibre.gui2.tweak_book.preferences import Preferences
+from calibre.gui2.tweak_book.widgets import RationalizeFolders
 
 def get_container(*args, **kwargs):
     kwargs['tweak_mode'] = True
@@ -390,6 +391,26 @@ class Boss(QObject):
         d.exec_()
 
     # Renaming {{{
+
+    def rationalize_folders(self):
+        c = current_container()
+        if not c.SUPPORTS_FILENAMES:
+            return error_dialog(self.gui, _('Not supported'),
+                _('The %s format does not support file and folder names internally, therefore'
+                  ' arranging files into folders is not allowed.') % c.book_type.upper(), show=True)
+        d = RationalizeFolders(self.gui)
+        if d.exec_() != d.Accepted:
+            return
+        self.commit_all_editors_to_container()
+        name_map = rationalize_folders(c, d.folder_map)
+        if not name_map:
+            return info_dialog(self.gui, _('Nothing to do'), _(
+                'The files in this book are already arranged into folders'), show=True)
+        self.add_savepoint(_('Arrange into folders'))
+        self.gui.blocking_job(
+            'rationalize_folders', _('Renaming and updating links...'), partial(self.rename_done, name_map),
+            rename_files, current_container(), name_map)
+
     def rename_requested(self, oldname, newname):
         self.commit_all_editors_to_container()
         if guess_type(oldname) != guess_type(newname):
diff --git a/src/calibre/gui2/tweak_book/ui.py b/src/calibre/gui2/tweak_book/ui.py
index 5c1ad54d62..c22580f289 100644
--- a/src/calibre/gui2/tweak_book/ui.py
+++ b/src/calibre/gui2/tweak_book/ui.py
@@ -327,6 +327,8 @@ class Main(MainWindow):
                                        _('Beautify all files'))
         self.action_insert_char = reg('character-set.png', _('&Insert special character'), self.boss.insert_character, 'insert-character', (),
                                       _('Insert special character'))
+        self.action_rationalize_folders = reg('mimetypes/dir.png', _('&Arrange into folders'), self.boss.rationalize_folders, 'rationalize-folders', (),
+                                      _('Arrange into folders'))
 
         # Polish actions
         group = _('Polish Book')
@@ -440,6 +442,7 @@ class Main(MainWindow):
         e.addAction(self.action_smarten_punctuation)
         e.addAction(self.action_fix_html_all)
         e.addAction(self.action_pretty_all)
+        e.addAction(self.action_rationalize_folders)
         e.addAction(self.action_check_book)
 
         e = b.addMenu(_('&View'))
diff --git a/src/calibre/gui2/tweak_book/widgets.py b/src/calibre/gui2/tweak_book/widgets.py
index 606e699bd7..c7a9ba0033 100644
--- a/src/calibre/gui2/tweak_book/widgets.py
+++ b/src/calibre/gui2/tweak_book/widgets.py
@@ -6,7 +6,7 @@ from __future__ import (unicode_literals, division, absolute_import,
 __license__ = 'GPL v3'
 __copyright__ = '2014, Kovid Goyal <kovid at kovidgoyal.net>'
 
-from PyQt4.Qt import (QDialog, QDialogButtonBox)
+from PyQt4.Qt import (QDialog, QDialogButtonBox, QGridLayout, QLabel, QLineEdit)
 
 from calibre.gui2.tweak_book import tprefs
 
@@ -46,3 +46,60 @@ class Dialog(QDialog):
     def setup_ui(self):
         raise NotImplementedError('You must implement this method in Dialog subclasses')
 
+class RationalizeFolders(Dialog):
+
+    TYPE_MAP = (
+                ('text', _('Text (HTML) files')),
+                ('style', _('Style (CSS) files')),
+                ('image', _('Images')),
+                ('font', _('Fonts')),
+                ('audio', _('Audio')),
+                ('video', _('Video')),
+                ('opf', _('OPF file (metadata)')),
+                ('toc', _('Table of contents file (NCX)')),
+    )
+
+    def __init__(self, parent=None):
+        Dialog.__init__(self, _('Arrange in folders'), 'rationalize-folders', parent=parent)
+
+    def setup_ui(self):
+        self.l = l = QGridLayout()
+        self.setLayout(l)
+
+        self.la = la = QLabel(_(
+            'Arrange the files in this book into sub-folders based on their types.'
+            ' If you leave a folder blank, the files will be placed in the root.'))
+        la.setWordWrap(True)
+        l.addWidget(la, 0, 0, 1, -1)
+
+        folders = tprefs['folders_for_types']
+        for i, (typ, text) in enumerate(self.TYPE_MAP):
+            la = QLabel('&' + text)
+            setattr(self, '%s_label' % typ, la)
+            le = QLineEdit(self)
+            setattr(self, '%s_folder' % typ, le)
+            val = folders.get(typ, '')
+            if val and not val.endswith('/'):
+                val += '/'
+            le.setText(val)
+            la.setBuddy(le)
+            l.addWidget(la, i + 1, 0)
+            l.addWidget(le, i + 1, 1)
+        self.la2 = la = QLabel(_(
+            'Note that this will only arrange files inside the book,'
+            ' it will not affect how they are displayed in the Files Browser'))
+        la.setWordWrap(True)
+        l.addWidget(la, i + 2, 0, 1, -1)
+        l.addWidget(self.bb, i + 3, 0, 1, -1)
+
+    @property
+    def folder_map(self):
+        ans = {}
+        for typ, x in self.TYPE_MAP:
+            val = unicode(getattr(self, '%s_folder' % typ).text()).strip().strip('/')
+            ans[typ] = val
+        return ans
+
+    def accept(self):
+        tprefs['folders_for_types'] = self.folder_map
+        return Dialog.accept(self)