Depends on your film and deposition method. For organic films we typically use a needle or something similar to make a scratch in the film and then measure the depth of this scratch. That's probably not gonna work for hard, inorganic films. During deposition you could cover some part of your sample and then measure the height diffence.
Dear all, please have a look at the following similar RG thread. I have pointed on a paper comparing major technique for film thickness measuring. My Regards
AFM is quite difficult for measuring thickness since it measures a very small area.
Of all the methods available, profilometry is the best . Make a scratch or other techniques to get a step and use stylus profilometer like Dektak or KLA-Tencor. Since it is a method which directly measures the physical thickness, very reliable.