Place a stone_button into /fill area
Add some random block of your choice to filter it out (stone for this example)

/fill x y z x2 y2 z2 #<- replace with proper coordinates air 0 destroy stone_button -1

BUG: Instead of destroying only stone_buttons it'll destroy the stone along with it.
WHEN: I found this out when I'm trying to destroy a pressed button and I'm executing it from a player. /execute @a ~ ~ ~ /fill ~4 ~4 ~4 ~-4 ~-4 ~-4 air 0 destroy stone_button 9