If you are aligning very critical machines and your laser system does not offer you the ability to apply vector tolerances, you can still do so manually, by keeping these criteria in mind:
The standard industry norms of 2 mils offset and 0.3 mils per inch of angularity at 1800 rpm equate roughly to vectors of 1.4 mils of offset and 0.17 mils per inch of angularity. Therefore, you can apply a sliding scale when you look at your misalignment results: If you have misalignment only in one plane (either vertical or horizontal), apply the full value of the standard tolerance; if you have roughly equal misalignment in both planes apply the more conservative values shown above to both. This way you will not exceed your vector limits in any direction. To find the vector limits for any RPM, simply take the square root of the standard limits.
Of course, none of this would be necessary if you have one of the better laser systems that features vector tolerances and calculates them for you automatically.