Most likely it cannot be scanned as it is in use. Trojan viruses run in the background like ordinary programs and usually load on startup of your PC.
Try booting up Windows then going to START, RUN and then type "MSCONFIG" then goto STARTUP and see if you can take the tick out and stop it starting up, some Trojans thought will start even if this tick is taken out as they bury deep in the system.
If that doesnt, work booting in SAFE MODE may startup without it running as SAFE MODE runs that minimum amount of services/apps/progs etc.
If your scanner cannot clean the virus you may have to find an app that can or remove it yourself plus registery entries. Post the name here and we'll try and help.