Yep, sure can. Ppl who write malware aren't stupid. They'll throw a couple of obvious files at you and one sneaky file. You get rid of the obvious and leave the sneaky there and quit looking for it. They especially like hijacking other programs and having malware sit dormant until the host program is used, you'll get infected, bypassing the internet download check. You finally get rid of the malware only to get reinfected every time you use the host. Malicious software is a royal pain to fully get rid of because most of the names are hidden by other files. It'll be called video.sys or other such important sounding name you'd not think was malware.
Only thing I can suggest is run malwarebytes with rootkit enabled, followed by Hitman Pro followed by Spybot: Search and Destroy.
All 3 are good, but relying on just 1 isn't good, they can only remove what ppl have sent to them in reports, so will not pick up on something new. By using all 3, hopefully at least one has had a report and will check for it.