This invention provides a system and method for finding patterns in images that incorporates neural net classifiers. A pattern finding tool is coupled with a classifier that can be run before or after the tool to have labeled pattern results with sub-pixel accuracy. In the case of a pattern finding tool that can detect multiple templates, its performance is improved when a neural net classifier informs the pattern finding tool to work only on a subset of the originally trained templates. Similarly, in the case of a pattern finding tool that initially detects a pattern, a neural network classifier can then determine whether it has found the correct pattern. The neural network can also reconstruct/clean-up an imaged shape, and/or to eliminate pixels less relevant to the shape of interest, therefore reducing the search time, as well significantly increasing the chance of lock on the correct shapes.