Extrapolating to 3D after assigning surface elevations

Hiya. Apologies if this is confusing. I have a few contamination areas that require refining. However if I refine these areas prior to 3D configuration and surface elevation assignment (using surface elevation points from GIS) I get errors as the model does not have an elevation point for all of the refined nodes. Additionally FeFlow struggles to do anything when I have all of my boundaries and contam areas refined accordingly. Has anyone else had this problem? Is there a way around it?
Cheers.
Deeds

If I understood you correctly, initially you have a 2D horizontal flow model. 2D horizontal flow models do not have nodal elevations. Instead, the aquifer top elevation as well as the aquifer base elevation are essentially elemental properties within an unconfined architecture. You may see that in the Data Panel.

If you are interested in assigning elevations for a 3D model I suggest to enter the third dimension (Layer configurator) and assign nodal elevations afterwards.