The shoot apical meristem (SAM) gives rise to above-ground organs and its establishment and homeostasis have been extensively studied. While a vast genetic network ensures the robust regulation of the stem cell population, two genes, CLAVATA3 (CLV3) and WUSCHEL (WUS), are key players. CLV3 is expressed in stem cells and encodes a secreted peptide to signal via transmembrane receptors to downregulate WUS, which encodes a transcription factor in the underlying organising centre. In turn, WUS directly activates the expression of CLV3 and the balance between the two molecules restrains the stem cell pool. The loss of CLV3 activity leads to an increase in SAM size, whereas the loss of WUS activity abolishes the SAM. The prevailing model is that the enlarged clv3 apex is composed of over-proliferating stem cells.Previously, our group coupled atomic force microscopy (to measure cell rigidity) and confocal microscopy (to determine cell identity) to show that stem cell identity correlates with increased stiffness. In this thesis, I show that in addition to altered mechanics, enlarged clv3 SAM also display severe defects in cell organisation. I find that cells in clv3 SAM are soft, instead of being stiff, as we had predicted in light of the model regarding the clv3 phenotype. Our data instead suggest that clv3 SAM differ mechanically from stem cells. I further investigate this contradiction using genetic markers for different domains of the SAM and show that clv3 SAM are in fact mosaic structures, made up of cells that simultaneously express genes that indicate an undifferentiated state and several that indicate multiple states of differentiation. Additionally, I show that the cellular makeup of mutant SAM is significantly altered from the wild type, with a misregulation of cell size in the outer cell layers. Furthermore, mutant SAM also display altered surface smoothness from wild-type SAM.Our working hypothesis is that in clv3 mutant SAM, cells undergo a constant stop-start phenomenon, where they cycle between stemness and specification, resulting in cell-level morphometric changes that generate the characteristic clv3 phenotypes. In summary, during my thesis, I have re-examined the role of CLV3 in morphogenesis at the SAM, and thus the CLV-WUS model of stem cell homeostasis. I conclude that the existing view in the field is limited, and that mechanical parameters need to be considered for a fuller understanding of stem cells.