Valencia were paired with the Swiss champions in Friday's quarter-final draw, after coming through their last-16 tie with Ludogorets 4-0 on aggregate.
Basel should provide a stern test for the Spanish side, having narrowly missed out in a place in the UEFA Champions League knockout stages after finishing third in Group E, despite twice beating Chelsea in the pool.
Murat Yakin's men secured a last-eight berth in the Europa League after coming from behind to defeat FC Salzburg 2-1 in Thursday's second-leg encounter, after the first match had ended 0-0.
Basel will now look to match last season's run to the semi-finals, where they were beaten by eventual winners Chelsea.
Perez insists Valencia will show the "highest respect" to their opponents, but is confident of progressing to the last four.
"There were teams in the draw, like Juventus for example, who were stronger but Basel are a good side," he said.
"I think we will stand up to the challenge but these are now the quarter-finals so we will have to be very careful.
"We have the highest respect for a team that has come into the competition from the (UEFA) Champions League, and what's more has won away against the likes of Chelsea.
"Added to that, in the last round of the Europa League, they managed to turn around a very difficult situation.
"But there are positive points from our side, such as playing the return leg at home. We need to maintain the tension and not relax a single bit. We must be optimistic in this competition, because the squad are looking on it as one of their objectives this season."
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