This paper reports a novel shadow mask aligner, which is capable of aligning planar with ∼1 μm alignment error as well as provision to compensate the wedge error by using movements of three precision linear actuators, spotted under optical microscope. The use of three points leveling also overcomes the common error of the upper assembly bending, which could occur with time after its continuous use. The reported wafer/mask holding mechanism is able to accommodate substrates of 3′ to 6′ diameter. The unique magnetic clamping mechanism after alignment has been successfully demonstrated. The fabricated system is useful for alignment of mask and wafer, as well as for other applications like nano-imprint and micro-contact printing lithography. In these cases, moulds/stamp is aligned with the patterned/un-patterned target substrate; to create complex 3D structures microassembly of independently fabricated 2D components by proper aligning and clamping. © 2020 IOP Publishing Ltd.