Both of these commands are Express Tools, but feel free to tell me if I'm asking in the wrong place. I'm using Civil 3D 2011.
If I use the flatten command I'm prompted to select objects (which can be a previous selction set, p) then I'm asked if I want to remove hidden lines. I usually say no and everything is great.
If I use the ssx command to create a selection set and filter by layer to select some objects and then use the flatten command and previous selection set created with ssx I get a dialog box asking me to "Confirm Export of AutoCAD Map Data" This appears to be the same dialog box I get when wblock'ing some objects.
I don't understand why this dialog box appears in this situation. Is this as designed and should I expect this behavior? Is there a better way to select objects by layer and flatten them entirely from the command line? I'm trying to include this process in a custom command.
I know it's bad form to answer my own post, but maybe this will help someone else.
I don't think this method is the preferred way to accomplish this, but it seems to work for now.
Instead of using the flatten command on the selection set created with ssx I'm using the move command twice. First move the objects using a displacement of 0,0,1e99 and then move the objects using a displacement of 0,0,-1e99. The 3dPolylines now are flat at an elevation of zero.