There are two prefixes spelled en-. One comes from the Latin suffix in-, has as its basic meaning into or onto, and chiefly forms verbs. Thus encapsulate means to put into a capsule, and enplane means to get on an airplane. This same en- also has the meanings to cause to be, as in endear, and to cover or provide with, as in enrobe. It sometimes has intensive force, as in entangle. En- has a variant spelling in-, which is why we have pairs like enclose/inclose and enquire/inquire.
1
The second en- goes back to Greek and means in, into, within. It occurs chiefly in scientific terms like enzootic, which is used of diseases and means affecting animals within a particular area.
2
Both suffixes change from en- to em- before b and p: embroil, empathy.