If you are seeing bumps on the top surface of your print which shouldn't be there, often at times invoking holes which penetrate the plain of the surface, then you are a victim of "Pillowing". You shouldn't have to deal with this issue, if you follow a few easy steps.
First of all make sure that your extruder fans are turned on when printing that top layer. Secondly, make sure that your outer print shell layer is at the very least thicker than 0.6mm (thicker than 0.9mm is recommended, especially on larger prints). Also take into consideration just how many layers you ar printing. If your layer height is set at 300 microns or more, then just a couple layers is not going to cut it, you will need quite a few layers anyhow to set up anything relevant of a dependable bonding shell to your print. A standard common sense quick fix is to take a look at your infill quantity. If you are printing a larger area print and your infill is inadequate to support the outside shell (you have large gaps the hotend must contiuously spread), then you need to increase you infill %. You can do this in the "Infill" section under the "Basic" tab after you click "slice" in CraftWare".
*PICTURE* screenshot of craftware infill section
If you follow these simple steps then your pillowing problems will soon go "poof".