Hi albehany, so I took a closer look at the cutout area and it definitely looks like you're constructing things in a "patch by patch" manner which is not optimal for NURBS modeling.

The way I'd recommend doing it is to try and work with solids instead. With that method instead of trying to build the cutout by drawing all the curves for it and then trying to build lofts or networks between pieces, you would instead start with a solid and have a second solid as a cutting tool and use boolean difference to cut the main object. Those steps look more like this (also see attached 3DM file):



So the main idea is the cutout comes from a boolean operation between 2 solids, rather than trying to build the cutout by individual surfacing operations. You want to work with 2D curves and solids as much as possible, you want to try and avoid drawing in all the 3D edges initially and then trying to build surfaces between all those edges. For NURBS modeling it's best if many of the final edges come from where 2 solids intersected each other from a boolean operation.

Now with this object you should be able to fillet the edges you wanted, up to a maximum of about 0.5 units - any more than that and it will run into the neighboring edge:






Hope this helps!

- Michael