Systems, dies, and methods are provided for processing pericardial tissue. The method includes positioning a die-cut assembly over the pericardial tissue, the die-cut assembly including a die having a plate, a the pattern, and an opening, the die pattern attached to the plate, the opening formed in the plate to provide access to the pericardial tissue, and measuring a thickness of the tissue through the opening. The die-cut assembly may be mounted for automated vertical movement, and a platen on which the tissue is placed is capable of automated horizontal movement. Different target areas on the tissue can be assessed by measuring the thickness through the die, and when an area is deemed suitable the die pattern cuts a shape therefrom. The system is useful for cutting uniform thickness heart valve leaflets, and can be automated to speed up the process.