With a mask plugged via, (a.k.a. Mask Filled or Non-Conductive Filled via), specific measures are taken to ensure the via is plugged and sealed with mask and the annular ring is covered. A common application for this is on a BGA design WHERE vias are commonly found in very close proximity to the BGA's SMD pads. The concern is during assembly, solder will wick away from the intended pad and flow down the via creating poor or non-existent solder joints.
TIP: If you require mask plugged vias, this must be specified in your fab print or readme.txt file. We will need to know the quantity, sizes and locations of the vias to be plugged so we can be sure all the required holes are plugged.