A method of and system for manufacturing a microstructure having high form accuracy and a manufacturing system is disclosed. On a rough motion stage having a predetermined positioning accuracy and a large stroke length, a fine motion stage having a small stroke length and a higher positioning accuracy is placed. First, the rough motion stage is moved to a desired position. By use of a mirror placed on a laser length measuring machine and the fine motion stage, the current position of a thin film member on the fine motion stage is precisely measured. This measurement value is feed-backed to a stage control device, and a difference between the current position and a target position is calculated by an error correcting unit. Thus, an error correcting instruction value is generated to move the fine motion stage to the target position. Thus, an error of the rough motion stage is corrected.