The study of changes in the atomic structure of a catalyst under chemical reaction conditions is extremely important for understanding the mechanism of their operation. For in situ environmental transmission electron microscopy (ETEM) studies, this requires preparation of electron transparent ultrathin TEM lamella without surface damage. Here, thin films of Pr1-xCaxMnO3 (PCMO, x = 0.1, 0.33) and La1-xSrxMnO3 (LSMO, x = 0.4) perovskites are used to demonstrate a cross-section specimen preparation method, comprised of two steps. The first step is based on optimized focused ion beam cutting procedures using a photoresist protection layer, finally being removed by plasma-etching. The second step is applicable for materials susceptible to surface amorphization, where in situ recrystallization back to perovskite structure is achieved by using electron beam driven chemistry in gases. This requires reduction of residual water vapor in a TEM column. Depending on the gas environment, long crystalline facets having different atomic terminations and Mn-valence state, can be prepared.