The shoot apical meristem (SAM) is a small population of stem cells that continuously generates organs and tissues. We will discuss here flower formation at the SAM, which involves a complex network of regulatory genes and signalling molecules. A major downstream target of this network is the extracellular matrix or cell wall, which is a local determinant for both growth rates and growth directions. We will discuss here a number of recent studies aimed at analysing the link between cell wall structure and molecular regulation. This has involved multidisciplinary approaches including quantitative imaging, molecular genetics, computational biology and biophysics. A scenario emerges where molecular networks impact on both cell wall anisotropy and synthesis, thus causing the rapid outgrowth of organs at specific locations. More specifically, this involves two interdependent processes: the activation of wall remodelling enzymes and changes in microtubule dynamics. This article is part of the themed issue 'Systems morphodynamics: understanding the development of tissue hardware'.