Yes. Each SQL Server instance runs a separate sqlservr process which can be viewed with a tool like Perfmon or Process Explorer (from SysInternals). The catch with Perfmon is it'll show sqlservr and sqlservr#(n-1) for n instances of SQL Server, meaning you'll have to do a bit of detective work to figure out which process belongs to which instance. Process Explorer makes it easy because you can the various handles the process has and at least two of them will point to the master database location.
K. Brian Kelley
@kbriankelley