For the most part, when you begin a 3D print, you simply let it go and wait.
Prior to getting that step is the important process of calibration.
Makerbot 5th Gen
The Makerbot's calibration process is semiautomatic. You initiate the process from the dial menu, under tools and then follow the on screen directions. The filament must not be inside the extruder. If it is, the Makerbot will ask you to unload it first. Once the calibration begins, the extruder will home its axes and then go to the middle. You have to tighten the appropriate screw under the build platform (as indicated by the on screen directions). A white light under the extruder will turn on once you have tightened or loosened it enough. This will happen on 2 more spots on the build plate and afterward, the process will repeat for additional fine tuning. If, for some reason the extruder light never turns on, try reattaching the extruder, or making sure the spring holding the nozzle will compress and decompress appropriately. If the nozzle does not move, then it may be jammed internally.
Makerbot 2nd Gen, Flashforge Dreamer and other Reprap Derivatives
For other Reprap derivatives, knock offs and such, the calibration process is manual. You have to initiate the process off the printer menu, and essentially do the same thing for the Makerbot 5th Gen's process. The key difference is that you are not guided by a light, you have to use a normal letter sized (or equivalent thickness) paper and slide it back and forth between the nozzle and build plate. There should be a fair amount of friction on the paper but you should still be able to move it around. This process is very subjective and can take multiple test prints to determine if the bed is relatively stable (less than 10% dimensional inaccuracy in any dimension.)