Make sure the spindle is adjusted correctly with respect to the table. Errors will show as steps between the passes. Hold the work down to the table of the machine having taken great care to make sure the work piece has no burrs and the table is free from dirt and dings (heaven forbid that you have any dings of course)and both surfaces are clean. Use your hands rather than rags to check. Clamp the work down using the 'T' slots - machine one side - reverse the plate - clean and reclamp - machine second side. Result is that both sides are now parallel. Any inaccuracies are due to the adjustment of the spindle axis to the bed of the machine. You can get fancy and correct the job by placing shimms under the thick end to compensate or re adjust the machine. Make checking the axis of the table to the spindle (tramming) part of your normal checks - particularly important for vertical mills where the last operation may have required an angle to be set.
In a production environment use hold down clamps of the toggle type either manual or air operated. Make a special jig if the edges also require machining. (Large right angle plate might do.) Clamp with toggle clamps or excentric cam blocks. In a production environment keeping the time to remount the work is key and keeping the surfaces clean is where much of the time will go. The vise and the supporting parralels are in my opinion just too akward to keep all the surfaces clean and any bits of dirt or swarf will lead to scrap parts.
Try and avoid thumping the table - a light tap yes! Also try and keep the number of interfaces between the table and the cutter to a minimum to save error being acumulated.
Most machining can be done without vise. The vise should be used to grip work that has parallel faces OR use packing pieces to ensure the work is held securely. My prefference would be to directly clamp to the table when ever possible. Just make sure you don't cut through into the table.
Hope this helps - Regards Pat