Systems and methods for automated laser microdissection are disclosed. In one variation, targeted biological material is manually or automatically selected and a transfer film is placed in juxtaposition to the location of an interior of a cut path. In another variation, a sample of biological material is mounted onto a polymer membrane which is then placed onto a substrate. Targeted biological material is manually or automatically selected and a transfer film is placed in juxtaposition with the targeted biological material on the side of the biological material. In yet another variation, a sample of biological material is mounted onto a polymer membrane which is then inverted onto a substrate. Targeted biological material is manually or automatically selected and a transfer film is placed in juxtaposition with the targeted biological material on the side of the polymer membrane. Then, an UV laser cuts along a cut path around the targeted portions of biological material in a closed cut path or a substantially closed cut path defining an interior and an exterior portion of the tissue sample. In a substantially closed cut path, bridges are left spanning the interior of the cut path and the exterior of the cut path. An IR laser activates at least a portion of the transfer film such that the transfer film in the vicinity of targeted portion adheres to the biological material interior to the cut path. The transfer film is then removed separating the targeted portions of biological material which are adhered to the transfer film from the remaining portion of the tissue sample.