Preheat oven to 400 degrees. Spray cups with canola oil. Arrange two prosciutto halves in each cup so that they cover the bottom, sides and are coming out the top of the cup. Add two to three pieces of polenta in a flat layer over the prosciutto, then add a slice of tomato. Gently press the layers down to ensure enough room for the eggs. Crack an egg over each cup being careful not to break the yolk. If the egg overflows out of the cup, scoop out some of the egg whites (otherwise the egg will create an air seal over the cup and the prosciutto will not crisp properly).
Bake on the center rack for about 13-15 minutes or until the egg whites are firm. Remove from oven and let cool a few minutes. Run a knife around the edges of each cup, carefully remove the egg nests and place on a serving platter. Sprinkle with half a teaspoon of pesto each and garnish with basil. Serve immediately.