We need some clarification here. Specifically, you say:
When I found the folders I was looking for, they had turned into exec files.
What turned into "exec" files? The folders, or the files inside them? And when you say they are "exec" files, what exactly are you seeing?
One possibility is that the files you created have all changed to look like this:

If that's the case, then most likely you have somehow created those files without an extension, which means that Mac OS X has no idea what they are. You need to add an extension at the end of the filenames: .html, .jpg, .pdf, etc.
One other possibility, which Tim mentions, is that you have connected this flash drive to a Windows PC that is infected with some kind of malware that has replaced all those files with malicious .exe files. These would not affect your Mac, but would certainly affect the data on the flash drive. Do the filenames end in .exe or .lnk?
If none of that matches what you're seeing, we'll need more details. Screenshots would help. Make a screenshot by following the directions here:
http://support.apple.com/kb/HT5775
Be sure no sensitive personal information is displayed. To add that image to a post here, click the camera icon in the post editor toolbar.