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This paper introduces a high precision 3D nanofabrication approach using ultrasonic vibration assisted nanomachining using an AFM operating in constant height control mode. Nanostructures with 3D features were successfully fabricated on PMMA film with the feature height manipulated through controlling the absolute heights of z-scanner in AFM. Two methods were used to move the AFM tip to create desire features, vector mode and raster scan mode. Relatively simple features, such as stair-like nanostructure with five steps was successfully fabricated in vector mode. Complex nanostructure with discrete height levels and continuous changes were successfully fabricated in raster scan mode. By carefully selecting the machining parameters, the feature dimension and height can be precisely controlled with only small variation from the designed value. Moreover, this paper explores the capability of transferring 3D nanostructures from PMMA film onto silicon substrate. After calibrating the recipe of Reactive Ion Etching (RIE) process, 3D nanostructures are successfully transferred to silicon wafer with controllable selectivity between PMMA and silicon. The results of fabricating 3D structures on silicon substrates show promising potential of many applications, such as mold preparation in nanoimprint lithography.