I know this should be simple to sort out using the download organizer or the Clean Installer but I have no idea how to use either. I just want to remove a few default replacement tops and bottoms and if I haven't just fixed it a maternity outfit replacement. The thumbnails are either the thing I downloaded or a maxis default which when I click on just makes the sim a floating head or a floating head with legs, should be a simple problem but I just can't find them and google is only showing me sims 3 answers.

There is no other way but to start testing and sorting as it isn't just one particular default that can cause that. I had invisible torso with Goopy's shirt and it was a default for that probably because it clashed with a custom file, a few defaults do that. All you can do is pull your defaults and put them back one by one until you find it.

They don't show up in game like on npc's or anything, so if its going to be difficult I'll just leave it. Is there any way to instead reset the CAS thumbnails to show the maxis original, so it might show what it is that hasn't replaced properly?

You make a test hood and dress the test sims in the borked clothes, pull your default folder and see if they are fixed. Hopefully your defaults are in one folder otherwise you will need to do the 50/50 method. If you have a lot of defaults put half back and see what happens, if they are all fine you know it's in the other half. If it's confined to say AM, then just test your AM defaults. There is no program or easy method but to test. I doubt you can change the thumbnail with the files in. You can try Ctrl right click but it will probably stay the same.

Sometimes defaults act weird. The other day I downloaded a default for my hula zombies or that outfit for my medieval hood and it messed up a default on a formal dress. You would think they have nothing to do with each other. Could be the default maker isn't aware of everything they need to check. So it is possible for two to clash, it would need to be in the same age range. Again I also had a CM outfit turn into a dress because of a girls default. It's as annoying as heck.