Methods of making monolithic three-dimensional memory devices include performing a first etch to form a memory opening and a second etch using a different etching process to remove a damaged portion of the semiconductor substrate from the bottom of the memory opening. A single crystal semiconductor material is formed over the substrate in the memory opening using an epitaxial growth process. Additional embodiments include improving the quality of the interface between the semiconductor channel material and the underlying semiconductor layers in the memory opening which may be damaged by the bottom opening etch, including forming single crystal semiconductor channel material by epitaxial growth from the bottom surface of the memory opening and/or oxidizing surfaces exposed to the bottom opening etch and removing the oxidized surfaces prior to forming the channel material. Monolithic three-dimensional memory devices formed by the embodiment methods are also disclosed.