“If there is malware on the system, I do not want to copy this as well”
I would suggest you download update and run the following programs
Malwarebytes' Anti-Malware Free Edition
SUPERAntiSpyware Free Edition
SpywareBlaster and keep it updated
SpywareBlaster is a prevention program, unlike most anti-spyware programs which
utilize a "Removal" approach after your system is already infected.
SpywareBlaster effectively prevents ActiveX-based spyware, dialers, browser-hijackers
and other Malware or potentially unwanted programs from ever installing on your system
in the first place.
Many users employ a multi-layered "prevent and remove" strategy by using anti-spyware
removal utilities in combination with SpywareBlaster protection
Once the above programs have completed do a defrag of the hard drive
Auslogics Disk Defrag 220.127.116.11
You should also do a defrag of the registry
Free Registry Defrag/Compact (Freeware)