Are they .doc files? Those are temporary files created by Word. The solution is, of course, to close Word. If some are still leftover after closing Word, you should at least be able to delete them once that they're no longer in use.
There are other programs that use tildes to indicate temporary files, but it's not altogether that common. If the files are temporary files for another program, and you find that you can't delete them even after you close the program, you might have a better chance doing it if you restart your computer and then delete them before starting up the program.