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First, instrument the exe or dll by command

vsinstr -coverage the dll/exe

second, start the performance monitor

VSPerfCmd.exe /start:coverage /output:"D:\Latest.Coverage" /cs /user:"Everyone"

at this time, we could check the status by running command:

VSPerfCmd.exe /status

third, start the windows service  and execute the test scenario.

Fourth, shut down the performance monitor tool by

VSPerfCmd.exe /shutdown

Trouble shooting:

on the 64 bit machines, you may could not get the coverage, instead it shows message:

  Empty results generated: No binaries were instrumented. Make sure the tests ran, required binaries were loaded, had matching symbol files, and were not excluded through custom settings. For more information see http://go.microsoft.com/fwlink/?LinkID=253731    

and in the event view, has error with source: VSPERF 

Unable to connect to monitor.  Make sure the monitor is started and in the correct mode.

Resolving by:

Run the above command from the tools for x64 machines, it located at

C:\Program Files (x86)\Microsoft Visual Studio 12.0\Team Tools\Performance Tools\x64