Micrometer-scale biochemical or topographical patterning is commonly used to guide the cell attachment and growth, but the ability to combine these patterns into an integrated surface with defined chemical and geometrical characteristics still remains a technical challenge. Here, we present a technical solution for simultaneous construction of 3D morphologies, in the form of channels, on porous membranes along with precise transfer of extracellular matrix proteins into the channels to create patterns with geometrically restricting features. By combining the advantages of microthermoforming and microcontact printing, this technique offers a unique patterning process that provides spatiotemporal control over morphological and chemical feature in a single step. By use of our 3D-microcontact printing (3DμCP), determined microstructures like channels with different depths and widths even with more complex patterns can be fabricated. Collagen, fibronectin, and laminin were successfully transferred inside the predesigned geometries, and the validity of the process was confirmed by antibody staining. Cells cultivated on 3DμCP patterned polycarbonate membrane have shown selective adhesion and growth. This technique offers a novel tool for creating freeform combinatorial patterning on the thermoformable surface.