How to cover vias with solder mask (solder resist) on Proteus
For you to cover the vias with the Solder Mask, you must disable the Guard Gap in the properties.

For example, below, I drew the outline of the board and filled it with "DEFAULT" type vias. Next to the image of the 2D board, the 3D visualization of it, allowing to verify that the vias are unprotected.



Then, you will click on the "Vias Mode" tool, select the desired vias type (in my case, "DEFAULT") and click on the letter "E" just above.



It will open the properties window of the respective via. You will change the Guard Gap option to "Not Present" and click OK.



Ready, this way, all vias of this same type will be covered by Solder Mask.