The morphology of Si(001) after carbon deposition of 0.05 to 0.11 monolayers (ML) was investigated in situ by ultra-high vacuum scanning tunneling microscopy (UHV-STM). The carbon induces a c(4x4)-reconstrutction of the surface. In addition, carbon increases the surface roughness compared to clean Si(001) (2x1). In a second step, the influence of the carbon induced restructuring on Ge-island nucleation was investigated. The 3D-growth sets in at considerably lower Ge coverage compared to the clean Si(001) (2x1) surface. This leads to a high density of small though irregularly shaped dots, consisting of stepped terraces, already at 2.5 ML Ge. Increasing the Ge-coverage beyond the critical thickness for facet formation, the dots show {105}-facets well known from Ge-clusters on bare Si(001) (2x1). However, they are flat on top with a (001)-facet showing the typical buckled Ge rows and missing dimers. This indicates that the compressive strain is not fully relaxed in these hut clusters.