Indium islands on molybdenum coated glass can be grown in ordered arrays by surface structuring using a femtosecond laser. The effect of varying the molybdenum coated glass substrate temperature and the indium deposition rate on island areal density, volume and geometry is investigated and evaluated in a physical vapor deposition (PVD) process. The joined impact of growth conditions and spacing of the femtosecond laser structured spots on the arrangement and morphology of indium islands is demonstrated. The results yield a deeper understanding of the island growth and its precise adjustment to industrial requirements, which is indispensable for a technological application of such structures at a high throughput, for instance as precursors for the preparation of Cu(In,Ga)Se2 micro concentrator solar cells.