Space-arranged arrays of pits on Si(001) substrates were prepared using electron-beam lithography and plasma chemical etching. The positions of pits were arrange to the square and hexagonal lattices with a varying spacing. It was shown that the location of three-dimensional (3D) Ge nanoislands subsequently grown on the pit-patterned Si substrates depends on spacing for the both lattice types. In the case of the small spacing Ge nanoislands are located mainly inside the pits, while for the larger inter-pit distance the groups of Ge nanoislands at the pit periphery is also observed. This effect is interpreted in terms of critical volume for the 3D island nucleation which is achieved at the pit periphery with the increase of Ge amount deposited per pit. The effect of nanoisland growth, first inside the pits, then at their periphery was reproduced by Monte Carlo simulations of Ge growth on the pit-patterned Si substrates.