Hi CK,
Open up the model. In the left window are the hex figures. Inside this window are at the right side Red Green Blue and Alpha - one column for each.
Watch out for the Alpha Channel column - FF is hexadecimal for 255, what is pure white and means opaque.
Windows and other semi-opaque materials have another value here.
To blank that part out, you need to move the material entries to the right and change the Alphachannel of the diffuse setting to "0".
I would also suggest to remove the shining: Setting for Specular is 0,0,0, 0 and Specularity 0 as well
Move the material back and save.
Note: please write down the number of the material you are changing (3. column), helps to find it again, when you have testflown it and blanked the wrong part out.
Note that the model may have several LOD-models, so you need to touch the windows of each sub-model!
Hope it helps!