A polymer-based flat, flexible and parallel optical interconnect has become an attractive approach for short-range data transfer. For such a device, a low cost fabrication technique is required for light couplers to redirect light from source to waveguides. Recently, we demonstrated a mask-less gray scale lithography process, which used a CMOS compatible polymer for a 45-degree mirror coupler. Polymer materials such as epoclad and AP2210B can be used to fabricate flexible substrates and waveguides, respectively. We propose an all-photopolymer lithography process to fabricate the flexible and parallel optical interconnect in conjunction with the mirror couplers. In the process, a buried polymer structure is used to precisely align the mirror coupler to waveguides, which make it possible to avoid an additional metallization process. However, the contrast of such buried fiducial mark is low since such the structure is a phase structure. As a result, it is not feasible to use the buried polymer structure as an alignment mark with conventional amplitude based imaging modalities. To increase the contrast of these buried alignment marks, we propose a feature specific alignment system for which the shape and depth of the buried alignment marks are optimized for phase-based imaging such as phase contrast and Schlieren imaging. Our results show that an optimized alignment mark provides a significant contrast enhancement while using a phase contrast imaging system compared to that of a conventional imaging system. In addition, we have fabricated an optimized alignment mark specifically for use with a Schlieren imaging system.