Alignment method for imprint method

An alignment system for determining an alignment between a stamp and a substrate in a substrate conformal imprint lithography process, wherein the alignment system comprises:

• a light source;
• a light sensor having an optical axis and configured to detect light from the light source redirected by the substrate wherein the optical axis of the light sensor is at a detection angle, α1, relative to the normal of the substrate of greater than 0°;
• a processing system communicatively coupled to the light source and light sensor;
• the alignment system configured to receive a calibration substrate having a refractive index n and comprising a first and second marker having a predetermined lateral displacement from each other, the first marker in the pair of markers being at a first predetermined vertical position within the substrate and the second marker in the pair of markers being at a second predetermined vertical position, different from the first predetermined vertical position within the substrate;
• the processing system configured to, when the calibration substrate is present within the alignment system, determine the first detection angle, α1, based on the first detected lateral displacement between the first and second marker on a calibration substrate;
• and
• use the determined detection angle to determine the alignment between the stamp and the susbstrate.