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Adjustable Axis Alignment Tool
Based on this http://www.thingiverse.com/thing:38300 and the wooden one Ultimaker now sends with new kits.
Each notch advances the pulley by 60 degrees.
You can test how square your axis are now by printing just one of these,
clicking it on and sliding it back and forth with two hands. The 6mm
axis shouldn't move. Or print 2 for calibrating/adjusting.
Print at 100% fill, you'll want a slicer that can fill thin walls.
Clean out the respective holes with a 6mm and 8mm drill bit.
This is the link to instructions from Ultimaker for aligning your axis http://wiki.ultimaker.com/Calibrate