Our paper presents a non-destructive thermal transient measurement method that is able to reveal differences even in the micron size range of MEMS structures. Devices of the same design can have differences in their sacrificial layers as consequence of the differences in their manufacturing processes e.g. different etching times. We have made simulations examining how the etching quality reflects in the thermal behaviour of devices. These simulations predicted change in the thermal behaviour of MEMS structures having differences in their sacrificial layers. The theory was tested with measurements of similar MEMS devices prepared with different etching times. In the measurements we used the T3Ster thermal transient tester equipment. The results show that deviations in the devices, as consequence of the different etching times, result in different temperature elevations and manifest also as shift in time in the relevant temperature transient curves