KeySurfaceFix, from Transoft Solutions (UK) Ltd, is an application for Civil 3D that will repair holes in a surface, or surfaces, in the current drawing.  

How to use KeySurfaceFix to Repair a Surface

Using Civil 3D, open the drawing with the surface containing holes.

Open KeySurfaceFix from the Transoft Solutions Apps >Surface Utilities>Surface Repair Palette (keyboard shortcut, KSRP).

This should scan the models and, on the Manage Holes tab, list the surfaces in the drawing and any holes found for each selected surface.

• Under Holes, check/uncheck each hole you wish to repair individually or, under Surfaces, check the box next to a surface to select all holes for the selected surface.
• To zoom to a surface in the drawing, select the surface name, right-mouse click and pick Go To from the menu.
• To zoom to a hole within a surface, select the hole(s), right-mouse click and pick Go To from the menu.
• Pick REPAIR SELECTED to begin the process of repairing the selected holes. 

Note: When repairing large or complex holes, it may only be possible to partly repair them in a single operation and so holes may still exist in the surface. It is good practice to re-scan the model to confirm that all holes have been repaired by selecting Scan All Surfaces for Holes, from the right-mouse menu under Surfaces.

The installer that ran when you downloaded this app/plug-in from Autodesk App Store will start installing the app/plug-in. OR, simply double-click the downloaded installer to install the app/plugin.

You may need to restart the Autodesk product to activate the app/plug-in.

To uninstall this plug-in, exit the Autodesk product if you are currently running it, simply rerun the installer, and select the "Uninstall" button. OR, click Control Panel > Programs > Programs and Features and uninstall as you would any other application from your system.