Yakushi-ji's layout is symmetrical, with two main halls and two three-story pagodas. The unique layout is also sometimes referred to as yakushiji-style. Yakushi-ji is geometrically planned out as a grid to replicate the Fujiwara capital to embody the new location. The Golden Hall rests in the middle of Yakushiji. Forward to the east and west of the golden hall are two pagodas symmetrically placed in order to bring attention towards the golden hall. The Golden Hall in Fujiwara resembles the Golden Hall at Heijo. Preservations of 18 column foundation stones found at Fujiwara show that the distance between each column are the exact length between columns at Heijo. In addition to the similarities in column width between the two, there are also identical staircases on each side of both temples. Discoveries of an underlying road system at Yakushiji at Fujiwara demonstrates that the temple was constructed around the road systems in the new capital. The East Pagoda replicated styles at the Heijo Yakushiji, with 12 granite column foundation stones found during excavations, whereas the West Pagoda demonstrated signs of being constructed during the early Nara period, after the capital had been moved, due to a different style. There are few remnants of the Fujiwara Yakushiji today, where the only visible markings of the temple are past foundations and columns of the Golden Hall.