A computer readable medium having computer executable code stored thereon, which, when loaded on a computer assembly, enables the computer assembly to control a method of transferring a substrate from a first substrate holder to a second substrate holder in a lithographic projection apparatus using a transfer unit based on transfer data available thereto, said second substrate holder having a surface provided with a first plurality of burls, the method comprising:
- providing a memory encoded with burl position data related to the position of said first plurality of burls on the surface of said second substrate holder and substrate position data related to a position and orientation of said substrate with respect to a second plurality of burls provided on a surface of a third substrate holder used in an earlier process step performed on said substrate;
- providing said substrate on said first substrate holder;
- measuring a position error and an orientation of said substrate provided on said first substrate holder;
- calculating orientation adjustment data based on said burl position data, said substrate position data and said orientation as measured;
- adjusting the orientation of said substrate in accordance with said orientation adjustment data as calculated;
- and
- transferring said substrate using said transfer unit from the first substrate holder to the second substrate holder in accordance with said transfer data and placing said substrate on said second substrate holder.