The attached picture shows how A , C and D layers are very rough and layers 

B are smooth. This seems to occur at the same levels in each of the models 

we printed.

Some are worse than others.

Solution:

Generally this problem is a function of three variables: 

• Temperature too high, try reduce 5 - 10 'C
• Flow rate too high, try reduce 5 - 10% or check that extruder calibration is spot on
• Print speed is too high, slow down the print a little. 
  

Try tweak one of those variables at a time and see if you can get it printing smoothly.

Over and above those factors some filaments can be more prone to this problem than others, try printing in a different colour and see if it helps. 

Finally one of the biggest causes of this problem is related to the nozzle size, slicer and slicer settings. You may see an improvement by using a better slicer like Simplify 3D, using a smaller nozzle size, changing your layer size and adjusting the extrusion width over height factor. The layer height can also play a roll. 

Essentially it is a case of fine tuning, but once you get it right the prints will come out perfect.