This letter solves a major hurdle that mars photolithography-based fabrication of micro-mesoscale structures in silicon. Conventional photolithography is usually performed on smooth, flat wafer surfaces to lay a 2D design and subsequently etch it to create single-level features. It is, however, unable to process non-flat surfaces or already etched wafers and create more than one level in the structure. In this study, we have described a novel cleanroom-based process flow that allows for easy creation of such multi-level, hierarchical 3D structures in a substrate. This is achieved by introducing an ultra-thin sacrificial silicon dioxide hardmask layer on the substrate which is first 3D patterned via multiple rounds of lithography. This 3D pattern is then scaled vertically by a factor of 200-300 and transferred to the substrate underneath via a single shot deep etching step. The proposed method is also easily characterizable-using features of different topographies and dimensions, the etch rates and selectivities were quantified; this characterization information was later used while fabricating specific target structures. Furthermore, this study comprehensively compares the novel pattern transfer technique to already existing methods of creating multi-level structures, like grayscale lithography and chip stacking. The proposed process was found to be cheaper, faster, and easier to standardize compared to other methods-this made the overall process more reliable and repeatable. We hope it will encourage more research into hybrid structures that hold the key to dramatic performance improvements in several micro-mesoscale devices.