Put butternut squash in the microwave and cook on high,until soft, 2-3mins.(to save time I buy all ready cut butternut squash at the supermarket and just boil for 15-20 mins until tender)Cut in half, scoop out seeds and cube.
Bring a large pot of water to a boil, add squash and cook until tender, about 15 mins-20 mins. Drain and mash.
In a 9x13 casserole dish, combine 3 cups mashed butternut squash, white sugar, milk and vanilla extract, salt, flour, eggs and 1/4 cup of melted butter.
Bake in preheated oven for 45 mins. or until set
In a medium bowl, combine crushed vanilla wafers, 1/2 cup melted butter, and 1 cup brown sugar. Crumble over top of cooked casserole and return to oven to brown.