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Calibre understands just about every ebook format out there. You could import all your ebooks into calibre, delete the original files (calibre sets up its own private files), convert those files that aren't in your preferred format to that format, and then have calibre export books in that format to wherever you want them, with understandable names. Or just leave them all in calibre and deal with them from there. In calibre, you can remove formats on a book-by-book basis, remove all instances of a specific format, or remove all formats except the one you prefer.
Even more important, in calibre you are dealing with your books as books, not as files. It doesn't matter what names their files have; what matters is the metadata of the books themselves. Think of it like fonts: on a Windows system, the font you see as "Somefont Italic" might actually reside in a file named SFI__.TTF down in the depths of a folder you never visit. But you never see that name -- you just install it, use it, and uninstall it, as Somefont Italic. It's an abstraction -- a font -- not a file. That's what calibre does for books. It doesn't matter if the file is 234956234.prc, you see it as "A Tale of Two Cities" in calibre, and deal with it accordingly. You might have that book in three different formats, but you don't have to look at 234956234.prc, 234956234.lrf, and 234956234.epub; you just have "A Tale of Two Cities" which, when selected, lists its available formats as prc, lrf, and epub.
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