Hi Jeff, did you possibly post the wrong model file?

The one that was attached to your model file does not seem to be the one in your screenshots above with the overlapping fillet surface areas, the one you attached seems to be 2 blocks stacked on top of each other:



Is the one that you're showing in the screenshots above with 2 fillet-like pieces overlapping right on top of each other from some other model that you meant to post?

But that kind of zig-zag intersection that you show there can happen if you've got 2 surfaces that are kind of barely skimming through each other in such a way that one is kind of only partially submerged in the other. That kind of situation tends to result in zig-zaggy intersections like that - if you've got something that kind of bubbles in and out of another thing that's actually what the physical intersection between them will tend to look like.

In situations like that you may want to trim the surface to what you know are common curves (possibly edges) rather than trying to intersect the surfaces directly which is what the booleans will try to do.

If you could post the model that you show in your screenshots above that would probably help me to give you some better advice.

A couple of things that I did notice about the one that you did post though is that you've got some planar areas that are diced up into some small plane fragments, like this here:



That's generally something that you want to avoid - there are some kinds of operations that will actually get confused with that, and it's a more complex model (more faces and edges) than is needed. So you usually want to just have one big plane in situations like that instead of a lot of little co-planar fragments.

You can fix those up by selecting all 3 of those top fragments and deleting them, leaving an open hole there like this:



Then select that object which now has a large planar opening at its top and run the Construct > Planar command to fill it in with a planar surface to get this result:




The Construct > Planar command can work in 2 different ways - if you have curves selected it will build a planar surface through those curves. If you have a surface object that has planar openings in it, it will build a planar surface and join it into those areas to make a cap there.


Then the other thing that I did notice about the model that you posted is that the ends of your fillet pieces here do not seem to have a very nice regular shape to them, there seems to be a small sudden swoop right near the end:






So there's something like a kind of sudden bulge or swoop near the end of that surface there, that may explain why it results in a zig-zag type thing if you are intersecting it with a fully regular-shaped fillet piece.

But try using the Trim command to cut the piece that is giving you the zig-zag result instead of using the boolean - if you have a curve you can trim your surface to rather than a grazing surface it can give you a better result.

For more advanced kinds of surface modeling like this kind of a project, where you're building some surfaces of your object individually, you tend to use Trim for that kind of a thing to work at the surface level as well - booleans are more focused on combining together solids and may have difficulty in situations where you're better of trimming with a curve rather than doing surface/surface intersections.

- Michael