A novel method relying on atomic force microscope (AFM) tip based nanomachining is presented to enable the fabrication of microchannels that exhibit complex three-dimensional (3D) nanoscale floor surface geometries. To achieve this, reciprocating lateral displacements of the tip of an AFM probe are generated, while a high-precision stage is also actuated to move in a direction perpendicular to such tip motions. The width and length of microchannels machined in this way are determined by the amplitude of the tip motion and the stage displacement, respectively. Thus, the processing feed can be changed during the process as it is defined by the combined control of the frequency of the tip reciprocating motions and the stage speed. By employing the built-in force feedback loop of conventional AFM systems during such operations, the variation of the feed leads to different machined depths. Thus, this results in the capability to generate complex 3D nanostructures, even for a given normal load, which is set by the AFM user prior to the start of the process. In this paper, the fabrication of different microchannels with floor surfaces following half triangular, triangular, sinusoidal, and top-hat waveforms is demonstrated. It is anticipated that this method could be employed to fabricate complex nanostructures more readily compared to traditional vacuum-based lithography processes.