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You must heat up the build plate to 115 degree, use the preheat option in the LCD display.
Then you start the leveling script, also in the LC menu.
Follow the guide and use a feeler gauge with 0.15mm. This is just to get a good starting point and also see if the build plate is flat.
If you do not have the dial indicator you use a 0.10mm feeler gauge instead for the instruction bellow.
Then start the guide one more time, but this time you will cancel it as soon the build plate and the nozzle has moved to position. You can choose any of them, but make sure you cancel the script before it will finish.
Now you will put on the dial indicator. You can move the extruders free to a position that you can mount the dial indicator holder.
Now you go back into the LCD and find the JOG menu. Here you will use the X and Y axis only. Do not use the Z axis.
move the carriage to a point over the left front screw. Watch out so the dial indicator not hit the frame.
Check the distance now with a 0.10 mm feeler gauge and make the adjustment so it will be 0.10mm gap between the nozzle and the build plate.
Move the dial indicator probe to the exact spot that the nozzle was that you did measure. This is very very important.
Now when you are on that spot, do zero the dial indicator. Now you got a reference.
Now use the JOG options to move the carriage on all the screws to start with and make sure the dial indicator now is zero over the screws.
Go over them a couple of times to make sure they are good. Make sure your build plate is still at 115 degree( it should be that).
After this your build plate is level.
Go over the build plate on the corners and the middle to check how good your build plate is. It should not be much different, it should be max 0.05mm different.
If its way over that then you need to contact the MBI for a replacement, MBI say they have a totally flat build plate now. I will soon get one new, for my others is warped, even if they are very little warped).
If all is good then they will be fine, but it also depending on your slicer, I think you should use makerware to start with. After all its very good and its MBI own software.