Custom homebuilders typically employ architects who will study the plot of land you've purchased and then design a home from the ground up using your specifications. The plan designed will be used once — just for your home — and because you're starting from scratch, the only limiting factors are budget and the requirements of your local municipality.
You have several choices when it comes to building a custom home: purchase a plot and then hire separately an architect and a home designer, or hire a building company that specializes in client-driven designs. In addition, make sure to check up on any builder you hire because many custom companies are small, doing only a few houses a year. Accountability and communication are key to getting your money's worth.