There is a certain number of PowerShell cmdlets I wasnt aware of. The complete list can be found in the Documentation.
I don't find the good step-by-step guide I once came across, but there are several others out there that descript how you connect your PowerShell to the Lync Server (like this).
I haven't tested any of these scripts, but Microsoft also provides a list of useful scripts to administrate Lync (link).
The problem I was initially looking for was: How do I hide disabled user accounts in the Lync Contact list. This can be done by ticking the checkbox "Hide user from global address list" in Exchange (Note: when this is done via e.g. VBScript it takes some time before the GAL is updated, in my case the account first vanished from GAL and the next morning it also disappeared from the Lync Contact List).