If you know definitely that the drive is infected your best option might be first to try get rid of the infection. You can dowload a offline version of Microsoft security essentials for example (http://windows.microsoft.com/en-us/windows/what-is-windows-defender-offline), you need to download 32 bit or 64 bit version depending on your operating system (32 bit works only with a 32 bit system disk and 64 bit 64 bit respectively). Another option is Parted Magic (https://partedmagic.com/), it has Clam-Av built in which can be used to scan the system.
With autoplay etc you might want to avoid plugging the hdd directly to another system without first atleast trying to get rid of the infection by more secure means.