Hello there!
I would like to bridge the gaps, i.e., yellow and purple face with an arch. I tried to do a simple bridge with ZModeler, but it doesn’t work.
I wonder if anyone could help me with this? Many thanks! 
Should work with Zmodeler. I just did it with a polycube with the corner removed to make astep like yours. Zmodeler Polygon Action : Bridge ; Target : Connected Polys, Circle. Drag up/down for number of spans and left/right for inward/outward curvature. Make sure when you touch the polygon face that the little orange line points from the purple to yellow poly if you touch the purple poly first (or vice versa). Move the pen tip closer to the purple/yellow intersection if not. It could also point from purple to green since they are also connected polys but you don’t want that. hth.
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Thanks for the solution! 