Water Jet Incremental Micro-Forming (WJIMF) is a novel alternative to Single-Point Incremental Micro-Forming (SPIMF). Instead of using a rigid tool to form the sheet metal, a high-speed and high-pressure water jet is employed to induce plastic deformation. Dieless WJIMF has the capability to form a variety of shapes, but the total depth of the formed shape, which is affected by several process parameters, cannot be well controlled. To alleviate this problem, supporting dies can be used. This paper systematically studies the WJIMF process with several types of micro-machined supporting dies to produce micro-scale shell parts with designed geometries. It has been shown that the design of the toolpath has a profound impact on the final geometry of the part even with the same supporting die. The experimental results suggest that supporting dies with different geometries require unique toolpath strategies to achieve high geometric accuracy. Furthermore, it has been determined that water jet pressure plays an important role in the plastic deformation of the metal foil and that inappropriate combinations of toolpath and water jet pressure lead to buckling which is not found in macro-scale Water Jet Incremental Forming (WJIF). A numerical model in ABAQUS was developed to simulate the process and predict part geometry.