Sure, no problem. No skyscrapers should be completely enclosed on the ground floor: pedestrians should be able to walk through to the other side in any direction. There could be several small clusters of shops at ground level. Newspaper kiosk, bagel shop, bookstore, Cheers bar, all the usual NYC kind of thing. Inbetween the storefront shops the under surface of the building wouldn't have to be flat and located one storey up: it could be vaulted to a considerable height of several storeys. Office space could begin on the second floor, but the floors wouldn't be joined into a continuous mass until the tenth or twentieth storey. The vaulted ceiling would consist of office windows so the effect would resemble the present canyons of Manhattan.