Selecting 2 individual surfaces will perform a surface/surface fillet operation, instead of an edge-based one.

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Normally fillets on a solid are applied to edges of the model. An alternative filleting mechanism is available by selecting 2 individual unjoined surfaces and running Fillet (you can use Edit/Separate to break a joined model up into individual separate surfaces). This style of surface/surface fillet is created by processing just the 2 surfaces instead of making the fillet try to follow edges, so it can succeed in places where the edge-based fillet will fail. This can sometimes be used to create fillets one piece at a time in difficult areas. The tradeoff is that these fillets will tend to require more manual trimming where pieces meet up while the edge-based filleting automatically trims and handles corner areas.