Residual stress engineering is widely used in the design of new advanced lightweight materials. For metallic glasses, attention has been given to structural changes and rejuvenation processes. High-energy scanning X-ray diffraction strain mapping reveals large elastic fluctuations in notched metallic glasses after deformation under triaxial compression. Microindentation hardness mapping hints at a competing hardening–softening mechanism after compression and reveals the complementary effects of stress and structure modulation. Transmission electron microscopy proves that structure modulation and elastic heterogeneity distribution under room temperature deformation are related to shear band formation. Molecular dynamics simulations provide an atomistic understanding of the confined deformation mechanism in notched metallic glasses and the related fluctuations in the elastic and plastic strains. Thus, future focus should be given to stress modulation and elastic heterogeneity, which, together with structure modulation, may allow the design of metallic glasses with enhanced ductility and strain-hardening ability.