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You can use boolean functions:
add, sum, ..
Suppose you chose cond (default layer) for your substrate.
If you want to cut a hole in your substrate, do this:
1) draw the whole substrate (ignore the hole at this step).
2) draw the hole, with another layer (say for example cond2) over your previous layer.
3) in this step you should subtract these two layers in order to make your hole.
go to Edit---> Boolean Logical --->
set the parameters like this:
"cond" "DIFF" "cond2" = "cond"
check mark these two box:
"delete original"
"delete original"
People are working in MEMS structure using ADS Momentum.
However it is 2.5D so it can not model the structure given above. specifically Bottom layer with 45 degree slant portion.
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