As Micro Systems Technology (MST) expands into new product applications, the present systems used to align substrates will have significant impact on yield and product performance. A new technique that ensures the best possible alignment has been developed eliminating misalignment effects from temperature, shock and mechanical movement. This new approach called Laser Welding maintains the precision alignment advantage of setting or freezing substrate position using laser technology to form micro bond spots while the substrates are in the alignment system. The transport tooling is no longer required to maintain alignment with mechanical clamping. This technique will allow device and process designers to scale the requirements for aligned substrate bonding to new levels. At the same time it will dramatically reduce the risk of misalignment from the present transport tooling associated with processes that are at the end of a cumulative build.