Strain engineering has been proposed as an alternative method for manipulating the electronic properties of graphene. However, the bottleneck for strain engineering in graphene has been the ability to control such strain patterns at the nanoscale. Here we show that high level of control can be accomplished by chemically modifying the adherence of graphene on metal. Using scanning tunnelling microscopy, the shape evolution of graphene Moiré blisters towards geometrically well-defined graphene bubbles was studied during the controlled, sub-layer oxidation of the ruthenium substrate. Understanding the dynamics of the oxidation process and defects generation on the Ru substrate allows us to control the size, shape and the density of the bubbles and its associated pseudo-magnetism. We also show that a modification of the same procedure can be used to create antidots in graphene by catalytic reaction of the same nanobubbles.