Programmable illuminators in exposure tools are employed to increase the degree of freedom in tool matching. A tool matching methodology is provided that utilizes the fine adjustment of the individual source pixel intensity based on a linear programming (LP) problem subjected to user-specific constraints to minimize the difference of the lithographic wafer data between two tools. The lithographic data can be critical dimension differences from multiple targets and multiple process conditions. This LP problem can be modified to include a binary variable for matching sources using multi-scan exposure. The method can be applied to scenarios that the reference tool is a physical tool or a virtual ideal tool. In addition, this method can match different lithography systems, each including a tool and a mask.