Not sure I can help, but...

First of all when you Publish to the Web, Publisher produces an index.htm
file and an index_files folder (not an index_images folder) that contain
your other .htm files and all the supporting graphics. Publisher uses VML
which means it also makes copies of any inserted image on a page in various
formats for different browsers. You can change some of the defaults by going
to Tools > Options > Web tab and unchecking "Rely on VML..." and "Allow
PNG...". And while you are there note that you can also opt to not use the
"Enable incremental publish to the Web". You do not change those files or
the content of the index_files folder, or the pages will not load correctly.
If you want to change your page(s), you make the changes in your original
Publisher file and produce new html output and upload it.

I note that you said that you linked to your thumbnails? If you insert a
thumbnail image, Publisher will treat that image just as any other image,
and will create copies. If you are trying to import an image from your
images folder, you don't insert the thumbnail...you import it along with the
link using the insert html code fragment tool to insert the code snippet
instead of a picture frame.

Now, I must admit I have no idea what you mean by "ctf directories" and I
don't know if this will help you answer your questions, but perhaps it will
help you ask a follow up question that I, or others here, better understand.

DavidF