Dynamic alignment of a wafer with a support blade that carries the wafer is provided by making a determination of an approximate value of an offset of the wafer with respect to a desired location of the wafer in a module. This determination is in terms of a statement of an optimization program, which effectively keeps an offset computation time period within a wafer transfer time period. By a method, and by programming a computer, the wafer is picked up from a first location using an end effector and the end effector is moved to transfer the picked up wafer from the first location past a set of sensors to produce sensor data. In the event of an unknown offset of a wafer, the picking up operation results in the picked up wafer being misaligned with respect to a desired position of the picked up wafer on the end effector. When the desired location corresponds to original target coordinates to which the end effector normally moves, the original target coordinates are modified to compensate for the approximate value of the offset. The end effector is then caused to place the picked up wafer at the modified target coordinates to compensate for the unknown offset and the misalignment. By determining the amount of such wafer offset using the optimization program, the probability of convergence to a precise value of the offset is higher than with non-optimization programs.