Pressing the enter key is like typing "a" or "b" or "z" on the keyboard. It causes the operating system to insert a character, or series of characters, depending on the operating system, to insert a newline. As the name suggests, this newline character is interpreted as creating a newline. But is an actual character, and in C it is represented by '\n'.
Note that to type anything for the program, you need to type all the letters, numbers, spaces, whatever, and then press the enter key. So yes, in your programs, you always, always, always keep entering that newline character. Depending on your program, you may have been discarding that character or ignoring it, but it exists, and you need to account for its existence.
Before you do anything with whitespace processing, can I see more code? You should be doing something like taking input with fgets, and then processing the input as you see fit.