rootkit found by avast- trojan.agent gen found by malwarebytes

I have been trying to figure this out for sometime so this goes back a ways. I still hope someone can help. Mar 15 rootkit found. Mar 16- no virus found. Mar 17- Rootkit found. mar18-21 no virus found. Mar 22, 24,35 all files couldn’t be scanned. mar 23 no virus found. I didn’t look at files and i didn’t have the pop up set if virus found so it was a few days after the rootkits were found before I knew they were there. I ran malwarebytes on Mar20 and found Trojan.agent. gen. it returned after deleting it . I have run kapersky anti virus free- nothing. I have run kapersky TDSSkiller- nothing found. I don’t know if my computers clean or not cause now Im getting “Some files can’t be scanned” and they have very different extensions, not something I would have password protected.
Does anyone have any words of wisdom or help. Thanks

What would help are the file names, locations of the detections by avast! and MBAM ?

Files that can’t be scanned are just that, not an indication that they are infected or suspect, just that they can’t be scanned.

By examining 1) the reason given by avast! for not being able to scan the files, 2) the location of the files, you can get an idea of what program they relate to and if the reason is legit. You may need to expand the column headings to see all the text.

If you can give some examples of those file names, the locations and reason given why it can’t be scanned might help us further ?