Fabrication of Micro-Electro-Mechanical-System (MEMS) using bulk silicon micromachining technology and semiconductor power devices often requires wafer processing from both the front and the back side of the silicon wafer. While transferring patterns onto one side of the wafer using photolithography, it is a requirement to align these with respect to already-formed patterns on the other side of the wafer. In order to do this, very expensive infrared mask aligners are generally used, which enables "viewing" of the patterns on one side of the wafer from the other side for the purpose of accurate pattern registration. In the present paper, a new technique is presented for front-to-back alignment. In this technique, identical square-shaped patterns called a "reference frame", having sides greater than the wafer diameter, are created on both the mask plates and used for pattern transfer on the two sides of the wafer. The regular device patterns are placed within this reference frame using the corners of the square as origins of coordinates. The detailed procedure of mask design and wafer-to-mask alignment is described. The technique has been successfully used to form common MEMS structures such as diaphragm and cantilever beams. Copyright © 2004 American Scientific Publishers. All rights reserved.