The shaped corneal/other tissue/bioengineered material trephines can create single or combination of shaped cuts and sections in cornea, sclera or any other tissue or bioengineered material of desired shapes, thickness, width, depth, radius, sizes/dimensions, measurements and configurations. It can create certain patterned or shaped cuts in tissue including but not limited to cornea and sclera/bioengineered material without using the femtosecond laser, especially in the case of cornea where at present the femtosecond laser is required for this purpose. A manual or motorized trephine allows creating cuts in different shapes, thicknesses, width, depth, radius, sizes/dimensions, configurations and measurements with single/multiple or combination of cuts. These configurable cuts give the advantage of creating shaped incisions/sections in the body of a subject as well as give the ability to create donor and recipient sections of cornea, sclera or any other tissue or bioengineered material of specific shapes and dimensions. It therefore gives the ability to create these shaped cuts and sections of tissue without the need for a femtosecond laser and also ability to cut through tissue that is not necessarily transparent.