Fillet on complicated geometry

So far you have done nothing wrong. Your on the right track.

It looks like you have made all the fillets using the FilletSrf command.
That’s a very good start. After making the fillets you need to trim the base surfaces and join them to the fillets.

If you were using Rhino5 all you would need to do is window select the fillets and use them as cutters for the Trim command and then Join everything and you would be done.

Since trimming is not as robust in Rhino after Version 5 what you have to do to make trimming work is select all the fillets and run the Join command and then run the DupBorder command. This will give you two curves which you can use as the cutters for the Trim command. After trimming the base surfaces all you need to do is join everything into a closed polysrf.

The comments I made about tolerance and tangency were in regard to the trimming and joining part. FilletSrf can make the fillets on your original model, but the loose tolerance and poor continuity will make the trimming and joining part a nightmare.

The scripts I posted links to work the same as the FilletSrf command (you set the fillet radius and click on 2 surfaces). The difference is it will make all the fillets in a string of tangent fillets. You don’t have to tell Rhino where each one goes like you do with FilletSrf. Just make one and it will do the rest if the base surfaces are tangent.
You should try making the fillets with Filsrf_JoinV2.py script it will not only make all the fillets but it will do the trimming and joining, also. Its faster than using FilletEdge and far more reliable and accurate for making a closed loop of fillets like you need.