Big profits for developers from rental apartment buildings are pushing builders into some difficult construction sites that have been overlooked for decades. When an executive at the Dermot Company, Stephen Benjamin, first submitted his company’s proposal to develop what had long been a couple of blighted blocks on the West Side, he had no idea the challenges that lay ahead.

In the end, Dermot and the other developer in the joint venture, Archstone, won the bid to build a new luxury rental apartment complex. Today, as the construction crews place the finishing touches on the Archstone Clinton building at West 52nd Street and 10th Avenue, no remnants remain of the significant obstacles they faced for three years there.

To be sure, vacant lots are a precious resource in New York City. But the city’s Housing Preservation & Development department is working with builders more than ever to come up with new ways to add to the Manhattan skyline.

Archstone Clinton, an imposing structure, consists of two towers separated by 52nd Street that rise over a tunnel for Amtrak’s Albany line. Ten times a day, a train bound for Albany passes up the West Side; another ten times a day a train returns to Pennsylvania Station.

The first year of apartment complex’s construction essentially involved the building of a new tunnel over the train tracks. Twenty times each day, the crew would have to stop their work to allow the train to pass. “It was a mess,” Mr. Benjamin said.

Another issue was the loss of an old theater space used by neighborhood companies. In their design Archstone Clinton had to incorporate community theater space for both the Intar Theatre and the Ensemble Studios Theatre.

Then there was the community garden, known as the Oasis, adjoining the site. Architects designed a public space to add to Oasis, a Hell’s Kitchen gem. “Between the railroad, the community theaters, and the garden, we had a big set of design parameters,” Mr. Benjamin said. “It was the most complicated, multi-faceted project we’ve ever been part of.”

Archstone Clinton’s unique integration of seemingly disparate design elements stems largely from encouragement by the city’s Department of Housing Preservation & Development. The department once oversaw a complete inventory of the city’s real estate after seizing abandoned lots and buildings during the 1970s and ‘80s.

“At one point the HPD owned 65% of the real estate in Harlem,” the department’s spokesman, Neill Coleman, said. “All those buildings were renovated and used for affordable housing. Now the city has to come up with more creative ways to provide such housing.”

Although Archstone Clinton is a luxury development, it signed on to the city’s popular “80-20” program: If 20% of a building’s units are affordable housing, the developer can float tax-exempt bonds.

The HPD recently held a design competition for another piece of land — in this case, in the South Bronx — that once held a railroad company right-of-way. They staged the competition in conjunction with the local chapter of the American Institute of Architects and received submissions from around the world for the 60,000-square-foot site.