Semiconductor nanocrystals serve as outstanding model systems for studying quantum confined size and shape effects. Shape control is an important knob for controlling their properties but so far it has been well developed mainly for heavy-metal containing semiconductor nanocrystals, limiting their further widespread utilization. Herein, we report a synthesis of heavy-metal free ZnSe nanocrystals with shape and size control through utilization of well-defined molecular clusters. In this approach, ZnSe nanowires are synthesized and their length and shape control is achieved by introduction of controlled amounts of molecular clusters. As a result of [Zn-4(SPh)(10)](Me4N)(2) clusters (Zn-4 clusters) addition, short ZnSe nanorods or ZnSe nanodots can be obtained through tuning the ratio of Zn-4 clusters to ZnSe. A study using transmission electron microscopy revealed the formation of a hybrid inorganic-organic nanowire, whereby the ligands form a template for self assembly of ZnSe magic size clusters. The hybrid nanowire template becomes shorter and eventually disappears upon increasing amount of Zn-4 clusters in the reaction. The generality of the method is demonstrated by using isostructural [Cu-4(SPh)(6)](Me4N)(2) clusters, which presented a new approach to Cu doped ZnSe nanocrystals and provided also a unique opportunity to employ X-ray absorption fine structure spectroscopy for deciphering the changes in the local atomic-scale environment of the clusters and explaining their role in the process of the nanorods formation. Overall, the introduction of molecular clusters presented here opens a path for growth of colloidal semiconductor nanorods, expanding the palette of materials selection with obvious implications for optoelectronic and biomedical applications.