This dissertation presents a number of sub-system designs for implementation into a multi-application, Multi-Scale Alignment and Positioning System (MAPS) developed in cooperation with the Center for Scalable and Integrated NanoManufacturing (SINAM). The production of the MAPS stage sub-systems as well as a novel Atomic Force Microscope (AFM) scanning system are discussed in detail from design to manufacturing and assembly. The MAPS stage is composed of a long range wafer positioning system with capacitance and laser interferometric position measurement. A side-to-side and rotational scanning system was incorporated into a bridge type frame that locates optics used to view moiré fringe patterns on both the wafer and stamp for alignment when using the imprint lithography module. Copper plates for eddy current damping of the stage were diamond fly cut for flatness along with a wafer chuck and stage capacitance gages. The wafer loading tool was re-machined to correct improper tolerances and a three pin adjustment system was integrated into the tool to ensure repeatable alignment of the wafer. Molds were designed and machined to produce more compliant gaskets for the imprint chamber and pin chuck on the imprint head to provide a tight seal around the wafer/stamp area for vacuum. An AFM was designed and built to enable feature measurement after an imprint has been made. During the operation of this AFM, the MAPS stage will be used to provide X and Y scanning motion of the substrate over a 10 mm x 10 mm window using laser position control to <1 nm. The AFM produces a 30 μm sweep at 4 Hz with the ability to measure a 10 gm tall feature on the substrate. From this design, a unique scanning mechanism is presented that comprises a four spoke cartwheel flexure element coupled to an arm, deemed, the "bat arm." The motion of this arm is controlled by dual Lorentz motors and small stationary magnets producing a 0.57 T magnetic field. Voltage input to the motors provides a controlled side-to-side sweep motion with no unwanted vertical motion that would damage the probe. A second flexure on the front of the bat arm is driven by a levered piezo-electric actuator to provide Z-axis movement of 10 μm. Applied voltage to the actuator is used to represent the probe position.