The Premiership outfit made the best chances in Romania against FC Astra Giurgiu but couldn’t convert any of them as a goalless draw saw Inverness eliminated 1-0 on aggregate.
Goalkeeper Silviu Lung proved to be a crucial player for the hosts, making a number of key saves to keep the Romanian side in front.
Hughes was happy with the way his team performed as they attempted to cancel out Constantin Budescu’s free-kick in Scotland last week.
He admits one area where they fell short, however, was in front of goal as they failed to make any of their opportunities count.
Hughes said: “Tactically we were spot on. (In the) second half we changed the shape and opened to have a go, it was just that final pass that has to be more clinical.
“I felt there were a few chances for us but we just couldn’t get that final ball over the line. I just feel for the boys, they put a lot of work in but we can learn from this.”
Around 400 Inverness supporters followed the team to Romania and Hughes feels his players did them proud.
He added: “It’s about the fans. They’ve had a blast, they’ve been well behaved and it’s for them. They’ll remember about that for the rest of their days.”