Aligned carbon nanotubes have been grown using microwave plasma enhanced chemical vapor deposition (PECVD). The carbon nanotubes are nucleated from iron catalyst particles which, during growth, remain adherent to the silicon substrates. By analysis with high-resolution electron microscopy, we observe iron silicide roots penetrating into the silicon substrate at the interface of the catalyst particles and the substrate, thus providing strong adhesion of the carbon nanotubes onto the substrate. The iron silicide roots assist in the attachment of the catalyst particles to the substrate and play a role in the evolution of the catalyst particle morphology and resulting base growth mode. Carbon nanotubes grown by microwave PECVD could exhibit superior electrical and thermal transport properties over other PECVD processes, so an understanding of the growth mechanism is important for utilization in device applications.