System horribly slow due to viruses?

It seems like my computer is still responding very slow, from program launch to just normal everyday tasks. Now I've done a scan with Avira AntiVirus, and it returned a few trojans which were deleted, and my firewall has blocked alot of attempted attacks. But I don't really know if this is just a virus issue, or perhaps a program issue, considering I have about 4GB left of space on my hard drive, and tons of programs, it would seem to be the logical answer but I need professional help here.