It is horrorfying the first time you see the number of malware files on your computer, Gary thousands is pretty normal if you never used an anti-malware program.
I use Spyhunter4 - not free, but I like it - very programmable to your needs - I never shut my pc down except to reboot if it gets goofy or to install Windows update. So I have Spyhunter4 do a deep search every morning at 3am.
Yesterday, something I clicked on in Facebook (I hate you Facebook) triggered Norton to give me a message and I ran Spyhunter4 right away, it found 38 issues that I clicked to delete. When I got up this morning, it had ran again and there were no issues.
I used Malwareplus for a long time, but after demo trying Spyhunter4, I like the user interface. So whichever malware type program you choose, set it up to run when you are not using the computer, so that you don't slow your surfing down as it does take up some resources and will drag a slow browsing session even slower.