Hi Sven,

 the verification under SEM, usual microscope and I suggest next time before
HF etching the interferometer
to check carefuly what indeed remained or is on the surfaces of the wafer.
As you wrote you found some roughness only on the top surface, it is closer
to go in the way to find out what the material/substance remained and it is
etched by HF.
I verified in my sources, that inter alia teflon, Chromium, Gold, Tungsten,
Si are not etched by HF.
Al is etched, there could be native oxide also. But native oxide is very
thin usually as you could find out in the mems talk mails, and from my
experience
oxide is etched very nice without leaving black spots etc.

Best Regards.