Peeling and Cubing Butternut Squash Before you start peeling and chopping a winter squash such as butternut squash, place it in the microwave oven and microwave at HIGH for about 2 minutes for a medium-size squash. This will make the squash easier to slice. Next, cut the squash crosswise into 2 pieces at the neck of the squash to reveal the seeds. Scoop out the seeds and the membrane using a spoon. You could also use an ice cream scoop or a serrated grapefruit spoon. Remove the peel from the squash using a vegetable peeler. The skin is tough, so it's sometimes hard to remove, even after you've softened it in the microwave. Remove the skin from both pieces of the squash. Cut the squash into round slices. To chop the squash, cut a round slice into 1-inch wide strips, rotate the strips a quarter turn, and cut into 1-inch cubes, or whatever size the recipe requires.