In this work, we demonstrate the selective area growth of high quality InP layers in submicron trenches on exactly (001) oriented Si substrates by using a thin Ge buffer layer. Antiphase domain boundaries were avoided by annealing at the Ge surface roughening temperature to create additional atomic steps on the Ge buffer layer. The mechanism of Ge surface atomic step formation and the corresponding step density control method are illustrated. The elimination of antiphase boundaries from the optimized Ge buffer layer, together with the defect necking effect, yield defect-free top InP layers inside the trenches.