How do I replace the non-air blocks in a 5x5x5 area?
have a 5*5 stone cube at spawn to clone to (assuming here you use 0 0 0 as the cube's coordinates)
/fill 0 0 0 4 4 4 stone // Fill temp area with stone
/clone x y z x2 y2 z2 0 0 0 filtered air // clone all air blocks to temp area
/clone 0 0 0 4 4 4 x y z // clone temp area to destination