It is possible that the malware damaged the PAF software on your computer. To fix it, download the PAF installer again from www.familysearch.org (click the button that says "Go to the previous site", and click the link there to "Download free PAF".
I suggest that you save the installer to your Desktop if possible, then try to uninstall the damaged software if you can. (Otherwise install the new copy over the old one.)
Your PAF data should be unaffected by all of this. The first time that you run the new copy of PAF, click the button to have it search for your data files. It should find them and be able to open them.