Wash the ceramic tile countertop with a household cleanser. Any dirt, wax or oils that remain will interfere with the bonding process, so be thorough.
Rough up the surface of the ceramic tiles with a belt sander fitted with 80-grit sandpaper. This helps the mortar adhere to the ceramic tiles.
Clean the ceramic tiles with a wet sponge, removing all the dust created by the belt sander.
Dry lay the granite tiles on the countertop with tile spacers between them, arranging the tiles so that the grout lines (the spaces between the tiles) of the granite tiles don't line up with the ceramic tiles' grout lines. When you are satisfied with the tile layout, mark the ceramic tiles at the edges of the counter with a pencil at the spots between the granite tiles.
Set the granite tiles and spacers aside. Snap chalk lines between the marks on the edges of the ceramic tiles, creating a chalk grid that you can follow when installing the tiles.
Spread thin-set mortar on the ceramic tiles with a notched trowel, dragging the notched edge of the trowel along the mortar as you work. Fill in only one section of the chalk grid.
Place granite tiles on the thin-set mortar, twisting the tiles slightly as you press them into the mortar. Use the chalk lines as a guide to keep the tiles straight, and place tile spacers between the tiles to create room for grout.
Repeat Step 6 and Step 7 for different sections of the countertop until it is covered in granite tiles. Allow the mortar to dry overnight.
Remove the tile spacers. Press grout into the joints between the granite tiles with a grout float. Once the grout has begun to set up, wipe the excess grout from the granite tiles with a wet sponge. Drag the corner of a damp sponge along all the grout lines, first in one direction, then the other, creating a smooth and even appearance. Allow the grout to dry overnight.