Two things to do:
1. Be sure that you downloaded CleanUp! from stevengould.org. Verify that the file size (in bytes) downloaded is exactly the same size as that reported on the download page.
2. After doing this, if you still get reports of a virus or spyware then contact the author/vendor of your anti-virus or anti-spyware software and report the problem there as a possible "false positive". Then let them further investigate.