Good news and bad(maybe) news.
The good news is that what you have outlined there is really pretty easy to set up.
you will need:
Your structure point file
FEMA's BFE lines
DEM/raster of the terrain data
Spatial Analyst license
Step 1. FEMA BFE lines need to be interpolated into a raster.
Step 2. Use this tool: Spatial Analyst Tools ->Extraction ->Extract Multi Values to Points: Point file is your structures file, load in both your terrain DEM and the raster of your water surface elevations.
This creates fields in your existing structures point file with the name of each raster and attributes it with the raster value at each point's location.
Step 3. Create a field in your structures file that you can then use field calculator to calculate the difference in.
So that is all you need to do to create the file you are looking for.
The bad news though is that based on what you say it is to be used for, its possibly not going to accurately give you the information you want. The reason I say this is that FEMA is either going to care about first floor elevations or the lowest adjacent grade which is probably not where the point was placed. If you have access to a structures footprint file there is a way that you can punch out holes in the terrain raster and then calculate the minimum value for each...Spatial Analyst->Zonal->Zonal Statistics(input feature is the structure file, raster is your terrain, stats type is minimum). Doing that and using its output instead of the terrain data in Step 2 should give you something a bit closer to what you are looking to do, but again it requires the structure outline which can be a royal pain to develop if its not available. Sometimes assessors or other county entities(planning dept maybe?) have first floor elevations. If you can get them in a table you could do a join based on address or parcel ID or something.
