The initial 3D shape is composed of three bodies. Assemble
Body.1 to Part Body.

Remove Body.2 from Assemble.1.
You obtain Remove.1:

Fillet Pad.3 's top edge.

Select Remove.1 and right-click Remove.1
object >
Change to Assemble. .
The
Change to Add...contextual command is available too.
You obtain Assemble.2. Note that the fillet
is still defined on Pad.3's top edge.

Select Assemble.2 and right-click Assemble.2
object >
Change to Union Trim...
The
Change to Add... and
Change to Remove...contextual commands are available too.
Click OK.
You obtain Trim.1:

Double-click Trim.1 and select the cylinder's
top face as the face to keep. You obtain this 3D shape:
