Perovskites have high potential for future electronic devices, in particular, in the field of opto-electronics. However, the electronic and optic properties of these materials highly depend on the morphology and thus on the preparation; in particular, highly crystalline layers with large crystals and without pinholes are required. Here, nanoimprint is used to improve the morphology of such layers in a thermal imprint step. Two types of material are investigated, MAPbI3 and MAPbBr3, with MA being methylammonium, CH3NH3+. The perovskite layers are prepared from solution, and the crystal size of the domains is substantially increased by imprinting them at temperatures of 100–150 °C. Although imprint is performed under atmospheric conditions which, in general, enhances the degradation, the stamp that covers the layer under elevated temperature is able to protect the perovskite largely from decomposition. Comparing imprinting experiments with pure annealing at a similar temperature and time proves this. Furthermore, imprint is capable of patterning the surface of the perovskite layers; lines and spaces of 150 nm width were reproducibly obtained under imprint at 150 °C. Moreover, a through-layer patterning is possible by using the partial cavity filling approach. Although not yet optimized, this simple way to define isolated perovskite patterns within a layer simply by thermal nanoimprint is of impact for the preparation of devices, as patterning of perovskite layers by conventional techniques is limited.