We report on a new method of inspecting deep microstructures manufactured in transparent media. Although their lateral dimension (tens of microns) do not exceed the diffraction limit for optical microscopy resolution, their deepness makes the nondestructive measurements practically impossible with presently available methods. We show that the optical vortex interferometer with a vortex generator can be used to differentiate between the samples of good and poor quality. The measurement system is simple and the interpretation of the results is straightforward.