Both classical activity mapping based on the induction of activity-regulated genes and novel genetic methods to label and control the activity of neurons indicate that memories are deposited in discrete neuronal ensembles in the hippocampus, amygdala and other brain regions involved in memory formation. However, the creation of a brain-wide map for engram formation and stability has proven to be a challenging endeavor that has been only partially solved. Among the methods to label active neurons, the Targeted Recombination in Active Populations v2 (TRAP2) mouse strain sticks out for enabling the precise and permanent genetic tagging of the neurons that got activated in a relatively narrow time window, such as during learning of an associative memory task. Here, we crossed TRAP2 mice with a recombination-dependent reporter that labels the nuclear envelope, which greatly facilitates the detection for automatic quantification of active cells and their separation using fluorescence activated sorting techniques. We used these mice in combination with iDISCO and novel analytical methods to evaluate the size, distribution, and stability of memory engrams in different brain regions, both in young and aged mice. The results of these analyses uncovered new aspects of engrams dynamics and identified new brain regions activated during fear memory formation and recall.