By Robyn A. Friedman

The process of designing a home can be a long and arduous one, particularly for a large or highly customized home. But building a custom home gives you the ability to make every design choice and to create a finished product that is unique and reflects the way you live.

Consider Dave Bacon’s experience. Mr. Bacon worked with an architect to design a 1,400-square-foot steel, glass and cedar “modern cabin” in Winthrop, Wash., a town in the Cascades about four hours north of Seattle. The 46-year-old software engineer spent $193,000 on a 20-acre tract with views of the Sawtooth Mountains and $485,000 to construct the home over two years. He paid an additional $55,000 to his architect, Seattle-based Ray Johnston.

“It was a big deal to make sure we had enough space for people to come visit,” said Mr. Bacon, adding that the home has only one bedroom but sleeps 11 by incorporating sleeping nooks, alcoves and a hanging bed outdoors. “But it would have been very hard to get all the sleeping arrangements otherwise. There are all these little details you can’t get unless you get your own architect.”

When working with an architect, the design process typically begins with an initial meeting at which the client provides the architect with a wish list, a basic overview of the home that includes details such as the number of bedrooms, baths and the overall style. After that, the architect will design several conceptual plan options consisting of floor plans that incorporate the wish list. Arriving at a preferred option typically takes six to eight weeks, according to Mr. Johnston, a founding partner of Johnston Architects.

Schematic design comes next, as does the creation of 3-D models that allow the client to walk through the house virtually. “When we produce these 3-D renderings and walk-throughs, it helps solidify for the client what the actual identity of the home is so there are no surprises when construction starts,” said Paul Fischman of Choeff Levy Fischman Architecture + Design in Miami.

Once the 3-D models are approved by the client, the design development phase begins and Mr. Fischman brings in consultants to complete the aesthetic details. He involves an interior designer, mechanical, electrical and plumbing contractors, an aquatic designer since all the homes he designs have water features and even a feng shui expert if the client so desires. “We have a consultant for everything under the sun,” he said. “Once we get the 3-D and the floor plans are pretty much frozen, they all come in, and we start turning the design into a real building.”

Engineers are involved at this point—a structural engineer to ensure the physical integrity of the building and a mechanical engineer to design the HVAC, plumbing and electrical systems to meet code—as is the general contractor, who often provides input. Once the construction drawings are prepared, the owner can apply for building permits, generally using an expediter, an expert who facilitates the process by working with the owner, the architect and the local municipality to finalize the plans. From start to finish—wish list to permit application—the process generally takes six to eight months depending on the size and complexity of the job, Mr. Fischman said.

Cost varies greatly depending on the particular project, location and the reputation and experience of the architect. Mr. Fischman said there are architects who design homes for $30,000 and those who charge $500,000. Mr. Johnston said that architects often charge a percentage of the cost of construction. He said his firm averages about 12% of the construction cost, and that charge covers the complete process, from the beginning of site analysis to the end of construction. He said some architects designing high-end homes charge up to 18%.

Here are some things to consider if you’re thinking about working with an architect to design a custom home.

Find the right architect for the job.  The best way to find an architect, like most professionals, is by referral or word-of-mouth, although many people hire architects whose work they have seen and admired. The local chapter of the American Institute of Architects might also be able to provide a referral. Remember that many architects, particularly those who design luxury homes, specialize in a particular style. Mr. Fischman, for example, designs Tropical Modern homes and said that someone wanting a Mediterranean design would go elsewhere. You will be working closely with the architect for years, so make sure your styles mesh. Some architects work independently, for example, while others are more collaborative.

Have someone on your side. Since most people building their own home lack the expertise to properly supervise the contractor, hire an expert to represent your interests. Kelly Mangold, a principal of real-estate consulting firm RCLCO, and a licensed architect, said that many architects will remain involved in a project they design during the construction process. “They can help manage the contractor to make sure things are done to the specifications on the plan,” she said. Another option is to hire an owner’s representative, a construction expert who will manage and execute the project on an owner’s behalf and whose fees vary based on the home size and type and on the duration of the project.

Focus on the details. A common mistake owners make is failing to pay attention to the plan. “Basically, they meet the architect and say they want four bedrooms and then let the architect make the plans,” said Pascal Nicolai, founder and chief executive officer of Sabal Luxury Builder in Miami. “Then, when the building starts, they say they didn’t realize the door was here or the wall was there, and they change the plan. Design everything up front to make sure you’re getting what you want in the end.”