Through horizontal and vertical excitations, we have been able to make a precision measurement of linear geometric optics parameters with a Model-Independent Analysis (MIA). We have also been able to build up a computer model that matches the real accelerator in linear geometric optics with an SVD-enhanced Least-square fitting process. Recently, with the addition of longitudinal excitation, we are able to build up a computer virtual machine that matches the real accelerators in linear optics including dispersion without additional fitting variables. With this optics-matched virtual machine, we are able to find solutions that make changes of selected normal and skew quadrupoles for machine optics improvement. It has made major contributions to improve PEP-II optics and luminosity. Examples from application to PEP-II machines will be presented