The nanostructure of micrometer sized domains (bits) in phase change materials (PCM) that undergo switching between amorphous and crystalline phases plays a key role in the performance of optical PCM based memories. Here we explore the dynamics of such phase transitions by mapping PCM nanostructures in three dimensions with nanoscale resolution by combining precision Ar-ion beam cross sectional polishing and nanomechanical Ultrasonic Force Microscopy (UFM) mapping. Surface and bulk phase changes of laser written sub-m to m sized amorphous-to-crystalline (SET) and crystalline-to- amorphous (RESET) bits in chalcogenide Ge2Sb2Te5 PCM are observed with 10-20 nm lateral and 4 nm depth resolution. UFM mapping shows that the Young’s moduli of crystalline SET bits exceed the moduli of amorphous areas by 11 ± 2%, with crystalline content extending from a few nm to 50 nm in depth depending on the energy of switching pulses. The RESET bits written with 50 ps pulses reveal shallower depth penetration, and show 30-50 nm lateral and few nm vertical “wave” like topography that is anti-correlated with the elastic modulus distribution. Reverse switching of amorphous RESET bits results in full recovery of subsurface nanomechanical properties, accompanied with only partial topography recovery resulting in surface corrugations attributed to quenching. This precision sectioning and nanomechanical mapping approach could be applicable to a wide range of amorphous, nanocrystalline and glass forming materials for 3-dimensional nanomechanical mapping of amorphous-crystalline transitions.