Like others mention in comments below, it's better to first design the shape how it should be in the end, fillets included, than doing them afterwards.
Also, in many cases, extruding an SVG works wonders. Just design the flat projection in something like Inkscape, interactively, and then import and extrude. You can do this for many shapes, then combine or subtract, etc.
But the other thing is, I have found that in many cases I don't need fillets at all; when printing small parts on a consumer-grade 3D printer, the relatively low precision of the printer is enough to round the edges.
Also, in many cases, extruding an SVG works wonders. Just design the flat projection in something like Inkscape, interactively, and then import and extrude. You can do this for many shapes, then combine or subtract, etc.
But the other thing is, I have found that in many cases I don't need fillets at all; when printing small parts on a consumer-grade 3D printer, the relatively low precision of the printer is enough to round the edges.