One way to minimize systematic errors from the laser system itself is to do what might be termed a “dose test”. This would involve make a very small design that has one or more features at and/or around your actual design's minimum feature size. Think something that can be etched in a minute or two. You develop your material settings on this design so that you can try many iterations of material settings within a shorter time frame (and you can likely fit many of them on a single sheet of your substrate) while keeping in mind that there are some things out of your control. Once you've determined settings that seem to work, do a test etch of the dose-test design prior to etching your actual design. If done properly, this can tell you if the etch will be up to
spec for your work. Try to hold as many systemic parameters constant as possible, e.g. the same position on the substrate, the same substrate piece, etc.