Systems and methods for aligning substrates that include microstructures. The microstructures may be electronic or micromechanical components. The system includes a first substrate having a first alignment structure and a second substrate having a second alignment structure. The substrates are positioned so that the first alignment structure contacts the second alignment structure without the substrates directly contacting each other, and one of the substrates is adjusted in relation to the other substrate until the first and second alignment structures lock into place. After alignment, the microstructures on the first substrate and the second substrate may establish a connection with or be positioned in near proximity to each other.