Preheat oven to 180 degrees celsius (fan-forced).
Line a 12 hole muffin tin with muffin cases.
Place the zucchini and carrot into the Thermomix bowl. Grate on Speed 8, 10 seconds (or until finely grated). Remove from the Thermomix bowl and place into a sieve. Squeeze out any excess liquid and set aside.
Place the cheese into the Thermomix bowl and grate on Speed 8, 10 seconds.
Add the shaved ham and chop on Speed 6, 5 seconds.
Place the zucchini, carrot, self-raising flour, eggs, milk, melted butter, salt and pepper into the Thermomix bowl and mix on Reverse, Speed 4, 5 seconds or until just combined (use the spatula to assist).
Spoon the mixture between the prepared muffin cases.
Bake for 30 minutes or until a skewer inserted into the middle comes out clean. Allow to cool completely on a wire rack.