It meant the 24-year-old scored four of United's seven goals on aggregate and left him just 12 away from the number Cristiano Ronaldo scored in the double-winning season two years ago.
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But the England striker is refusing to look too far ahead, and insists his major priority is looking forward to the last eight draw on Friday week.
"I am delighted to get two more goals but I have not set myself a target. I just want to keep scoring," said Rooney.
"Overall, it was a great result and we are delighted to get through.
"Now we can just look forward to the draw and see how it goes from there.
"There is no preference. They are all difficult games at this stage of the competition."
United already know Lyon, Bayern Munich and Arsenal are potential quarter-final opponents, while holders Barcelona, Inter Milan, Chelsea and Sevilla appear to be the strongest sides left in the other half of the draw, which is concluded next week.
However, after ripping apart the seven-time winners in clinical fashion last night, it is the rest of Europe that needs to be wary of United, who are bidding to reach a third successive final for the first time in their history.
"The first goal was vital," said Rooney. "We set out to get an early goal to kill the game off and when we got it we shattered Milan's confidence. That was the major turning point."