Assuming it's a windows VM since you mentioned windows commands you will need to create a windows target for it and then you can use windows commands against that.
You can create the target manually in the definitions->target area or you could create the target in a process/automatically via the Northbound Web Services and a call to the TARGET WSDL.
If you want more info on that, check out my blog on the NBWS:
https://supportforums.cisco.com/blog/9914016/pondering-automation-how-i-saved-bundle-switching-cpo
--Shaun
--Shaun Roberts
Principal Engineer, CX
shaurobe@cisco.com