Skyward Sword HD takes with it a few special killing moves from its brother, The Legend of Zelda: Twilight Princess, and this is never a bad thing. One such move is the Fatal Blow, which can kill most enemies in a single attack.
To do this Fatal Blow depends on what control scheme you are using to play the game, motion controls, or button controls.
If you are using motion controls, to do a Fatal Blow is super straightforward. When an enemy has been knocked back on the floor, this could be a Bobokin lying prone or a giant spider on its back. All you have to do is Z-target the creature by holding down the ZL on the left Joy-Con (so there is a marker above the enemy's head) and then flip your wrists upwards towards your chest. So the Joy-Cons that were once horizontal are not vertical. If done correctly, an animation will play with Link jumping in the air and stabbing his sword into the creature. But this is time-sensitive. The enemy will not stay prone forever.
If using the button control scheme, it's a tad bit more tricky. Like above, make sure that the enemy is lying prone or on the floor. Then using the right analog flick it using the following combination: Up, Down, Up, Down. If done correctly, the animation will play with Link stabbing his foe. Though, just like using motion controls, this is time-sensitive.
We have more the Legend of Zelda guides here at PGG.