Malware is an all-inclusive term, intended to include any software or functions normally associated with spyware, adware, viruses, foistware etc. Although some specific files may be designated as "virus" nowadays, the malware coders take advantage of any methods they can to succeed in infecting and misusing the systems of their victims. So a trojan downloader can be used to trick the user into allowing the infection computer access, which then delivers/installs active malware components, and included in these can be files with "virus" functioning of self-replication.
What I read in your request here is that regardless of the designation used, your computer has active infection there which needs to be addressed.
To just repeat what I post in some other requests here, too little info and too complex a scenario to honestly suggest this or that tool or repair here. I would suggest posting a request at an available free infection removal forum to get your system cleaned up. I can either assist you at mine, or you can just yahoo web search "hijackthis free help" or words to that effect to locate one of the locations where you can receive assistance. Jintan