First make sure the arm is calibrated. (Note: if the arm is calibrated and you're still seeing the uneven surface, the calibration was probably not tight enough). Also, make sure the arm is on a table that will not shake and that the object you are scanning is clamped down.
After you complete the scan, exit the plug-in. Highlight your scans in the Model Manager and go to Alignment>Scan Registration>Global Registration.
Click Apply to run Global Registration. Global Registration fine-tunes the roughly-aligned orientation of two or more scans so that they match up. (Note: Global Registration for fine adjustments with registering scans. If your scans are farther apart, use Manual Registration. See What are some tips for using Manual Registration?)
After registering, select your point objects and go to Points>Combine>Combine Point Objectsto combine them into one point object.