A multilevel microcontact printing (μCP) system that avoids the use of optical alignment and precision manipulation equipment is demonstrated. Most of the complexity is transferred to the poly(dimethylsiloxane) (PDMS) stamp itself by forming the features, a mechanical self-alignment mechanism, and an elastic membrane by wafer scale replica molding on a Si master. Flexible 50-μm-thick photoetched stainless steel sheets are bonded to PDMS prior to demolding to improve the mechanical stability. The Si master itself is made using conventional MEMS fabrication tools such as photolithography, reactive ion etching, and anisotropic wet etching. Self-alignment is achieved by introducing protrusions on the stamp that mate onto corresponding grooves on a machined substrate. Complete 10 mm ×10 mm prototypes are fabricated, and six-level μCP is demonstrated with an average layer-to-layer misalignment of 5−10 μm.