You've got yourself into a sticky situation here. First off, you may want to remove doubles by hitting "W" in edit mode then selecting "Remove Doubles". You can alternatively find this setting in the toolshelf (toggle by pressing "T"). Second, some of your normals are facing the wrong way, which can affect extruding. Recalculate them by selecting all in Edit Mode then by pressing "Ctrl + N". Third, you've already extruded the layout, so selecting all then extruding won't work. Select only the top faces by going to the top view (NUMPAD 7) and Orthographic mode (NUMPAD 5) then box selecting by pressing "B" then clicking and dragging to make a box over the entire layout.
You can exit Orthographic Mode (NUMPAD 5) and top view at this point. Now, since the model is already extruded, you can just move the top layer along the Z axis by pressing the blue arrow or by pressing "G" then "Z". However, you can still extrude it if you'd like, it would just create more polygons, thus extending render times a bit.
Hoped this solved your problem. Happy blendering :D