Microfabricated filters utilizing a bulk substrate structure and a thin film structure and a method for constructing such filters. The pores of the filters are defined by spaces between the bulk substrate structure and the thin film structure and are of substantially uniform width, length and distribution. The width of the pores is defined by the thickness of a sacrificial layer and therefore may be smaller than the limit of resolution obtainable with photolithography. The filters provide enhanced mechanical strength, chemical inertness, biological compatibility, and throughput. The filters are constructed using relatively simple fabrication techniques. Also, microfabricated containment wells and capsules constructed with such filters for the immunological isolation of cell transplants and a method for constructing such containment wells and capsules. The pores of the wells and capsules are large enough to let a desired biologically-active molecular product through, while blocking the passage of all larger immunological molecules. The containment wells and capsules provide enhanced biological compatibility and useful life.