We report here a numerical study of wave-interaction with an array of idealized coral-growing units, with each unit being a thin-walled, perforated, hollow, cylindrical structure. This study focuses on the effects of four layouts on wave transmission and energy dissipation. Numerical simulations are performed using a Boundary Element Method (BEM), with the energy dissipation by the perforated plates being parameterized in the potential flow solver. Due to wave scattering by 3D units, wave transmission and energy dissipation cannot be evaluated by transmission and reflection coefficients calculated by local wave amplitudes alone. To evaluate the wave transmission and energy dissipation, we use the energy flux across vertical 2D planes in the far field instead. Among the four layouts examined in this study, one layout has units closely arrange in rows, similar to submerged breakwaters, and other layouts all have wider space between units. Results showed that the layout has minor influences in wave transmission and energy dissipation, unless the units are closely arranged in rows. Factors other than layouts should be considered to optimize the energy dissipation by a patch of coral-growing units.