Mark3D

To trouble shoot I change the color and line weight of the elevation data so it stands out  then look to see if you have overlapping elevation data or even turn all layers off and just show elevation data and study it my guess is you will have elevation data set wrong to cause the problem

You have posted a dwg file they need your .plan file 

solid railing type

Watch some training videos on roofs railings and rooms 

Have a look at this file it should get you moving in the right direction 

As-Built.plan

Terrain imported you just need to move it across to your house as you gave me no info as to placement and set the height as described in above post remember to rebuild terrain

21-144 Floor Plan Final Design.zip

The merged cad if you are going to try 

13159-BNDRY & topo.dwg

The terrain does not copy it converts to cad,  so either you can watch the video and i can share the merged cad, or you can or share your plan file and i can re import the terrain

i had a go it might get what you want , I had  to merge the to files then did the terrain import as shown in this video  also to raise and lower the terrain to suit building height adjust subfloor height above terrain in terrain specification dialog

Import a Surveyor DWG file for a Site Plan or Terrain Perimeter (chiefarchitect.com)

Terrain import.plan

Here is a file with auto roof it may help you

1467467882_existing-dormer-fix(1)Mark.plan

Watch this you tube video

Have look at this plan i rebuilt the roof with some other changes noted in the plan, its like you have found a condition that is tricking chief

1467467882_existing-dormer-fix(1)Mark.plan

If understand set ceilings to 9’ and lower your roof planes to 60” and that should cut your walls down

if you give me a plan with your model i will put the terrain in it if  you want i also had no end of trouble with the cad file i think it has something to do with the contour line being blocked not sure 

upload your home designer file and i will have a go at it 

I wonder if you use the room structure to set deck framing leave a airgap where roof components would be add a framing layer floor joist  then manually draw roof plane in airgap and  framing then convert framing and roof plane to a symbol as that will stop the roof plane messing with the structure

I  was try to fix this while Eric was making his very helpful video here is my file if it helps

Plan 1556 with porch (A).zip

I think you have unknowingly inserted a second floor delete  that with your floor tools and thing should start working also you have lots of unconnected walls witch wont form rooms you need all rooms wall connected to form rooms

hopefully this will work in your software as i am guessing you using home designer brand not chief architect as this forum is for

i think you have been using the eyedropper paint tool try changing the materials back the there defaults also remove the room wall coverings things should look better  after that

use a terrain hole

Not sure but make sure your video card drivers are up to date

With that interior office that has a gap i dragged the lower wall to the ridge the the gap was gone give that a try 

Have a look at the attached plan your exterior walls need to be setup like in real world also the interior layer is the main layer  i reset the main layer so it has altered your exterior size so perhaps use your model and reset so you can see what is going on 

the gap on that interior wall not sure these guys here will know i am sure

1527905163_Testhouse mark change.plan

The bonus room walls are marked as no room definition turn that off

Try the terrain hole tool