how to change substrate

I don't know what you want to do...

In ADS it is very easy to remove a susbtrate model, just click on and delete.

In layout---> Momentum---->Substrate----> Create/Modify

I want to remove part of the substrate not the whole substrate. Say, notch 1/3 from the center.

Any detail file for our reference?you can draw some object and define the substrate between layers

Like the one in the picture.
I want to remove some part.

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"

Now, you have your substrate with the hole.

hope that helped.

I don't think Momentum can simulate MEMs structure.

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.

Can I use HFSS to do it?

HFSS is ok.