A custom home is one that is especially designed to meet the specifications of the person who commissioned it. Stock building plans are not custom designed; the same plan may be sold to many different people.
Frequently a builder will customize stock plans by changing details. The builder may change the type of siding, move a doorway, or even add a dormer. However, the house is not truly a custom home unless a designer (usually an architect) has closely studied the land and interviewed the clients to create a one-of-a-kind home that is tailor-made for the people who will live there.
To build a custom home, you will need a building site and an architect or a professional home designer. A builder who specializes in custom homes (not a Production Home Builder) may also offer design services.