need help running checks on secondary HD

My main computer stopped booting so i took the hard drive out and put it in another computer as a slave so its not the main C: drive. I down loaded all of the recommended programs to scan for malware/rootkits and viruses but most of them only scan the main C: drive and not the HD i have hooked up that im trying to fix. Are there any programs similar to ccleaner tdsskiller and hitmanpro that will let me check that drive or is there a way im not seeing in the programs options? Thanks in advance for the help