There are two problems that make filleting fail.
First of all your surfaces are non-periodic closed surfaces. You probably want them to be periodic.
A periodic surface is closed but essentially has no beginning and end. A closed surface that is non-periodic (like yours) can have discontinuities at the seam. And you want surfaces that are tangent continuous at all seams (edges) that the fillet has to cross.
You can use MakePeriodic command to make the surface periodic before you start filleting. Or create the surfaces as periodic to begin with.
The other problem is that fillets will fold in on themselves if you try to put them on surfaces that have concave curvature of less than the fillet radius. In other words, A fillet of 1mm won’t be able to cross over a dimple in the surface with curvature of less than 1mm. In your example the smallest radius that can be supported is about .38 mm. You can use CurvatureAnalysis with minimum curvature set to a range of 0.3-2.0 to find the areas where the curvature radius is low. In the enclosed file I edited the surfaces so that a fillet of 1mm can be supported.
periodficSurfaces.3dm (146.9 KB)