Methods for compression molding through holes in polymer layers are provided, as are the resulting patterned polymer layers. Two key aspects of the invention are provision of a mold and substrate having different mechanical hardness, and provision of room for local flow of material. These aspects of the invention facilitate formation of through holes by compression molding that are not blocked or partially blocked by undesirable material. These polymer layers can be formed into three dimensional patterned structures by bonding patterned layers together. Since the layers include through holes, a three-dimensional polymer pattern can be formed. These patterned polymer layers and three dimensionally patterned polymer constructs have a wide variety of applications. For example, these constructs can be used for fabrication of micro-fluidic devices, and/or can be used for various medical and biological applications including drug delivery devices and tissue engineering devices.