The corners are the problem. Basically the bottom of my model is a rectangle with rounded corners and the top is a pillow. I have been unable to keep corners from flattening and pinching. Any help would be greatly appreciated.
Are you trying to create the loft between 2 sketch identities or are you trying to create a loft between 2 surfaces or a combination of the two?
If you are trying to create a solid loft between 2 sketch identities the problem could be the connection.
I.e. if you have a rectangular shape with rounded corners you have 8 points on your bottom sketch. Lofts like to connect an even amount of points. So if your top model is a organic shape / "Pillow", I am going to assume this would be a spline.
To help your loft you could add more points on the spline using the spline properties. (this is different than adding a sketch point on the spline)
Then position them so the loft will lead the surface as you want it.
A little easier would be to have a rectangle without rounded corners(4 points) and loft them to your spline with 4 points (I.e. if the pillow is square these would be on the corners) and then add a fillet on the edge.
If this isn't a solution could you provide us with some more information, a picture or the file, so the forum has a bit of context.
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