Button said it had been a "tough day", adding: "It would have been nice to get more testing done.
"I've been doing a lot of work making sure I'm comfortable in the car. I wasn't quite where I wanted to be. I was quite high in the car and uncomfortable.
"I had to change a lot within the car. I fit well now and feel comfortable with my head in the car now."
Button added: "This is not the best circuit to get a feeling of how the cars going to be during the season - it's very different to any other circuit to race on, the balance is very different.
Testing 'frustrating but useful' - Button
"We can say that Ferrari are fast but we don't know how fast. You can't do those times if you're not competitive.
"We don't know what fuel they're running when they do those times but their slower runs with high fuel were still reasonably good. But it's wrong to talk about who is quick and who isn't."
Winter testing times are notoriously unreliable indicators of form because fuel loads, tyres and track conditions can make a significant difference to performance.
Alonso, whose appearance at the test brought a crowd of 30,000 spectators, said he was "very, very cautious" about judging the pace of the car from his first day's running.
We are not as quick as Ferrari and Lewis Hamilton looked quick yesterday so it looks like we've got a bit of work to do
Ross Brawn Mercedes team boss
"It was a very good day," the Spaniard said, "because I found the car very easy to drive because Felipe was running two days and I've been taking this information from him and it was a help. Let's wait."
But Mercedes boss Ross Brawn admitted that Ferrari appeared to have the quickest car in Valencia and added that his team were struggling a little.
Brawn told BBC Sport: "On full tanks yesterday (on Tuesday) we didn't look too bad but we're a little bit off on pace and (there are problems with) the handling and balance of the car which we can fix for Jerez (testing next week). We know what the problem is.
"Of course the other teams will be progressing as well. We are not as quick as Ferrari and Lewis (Hamilton) looked quick yesterday so it looks like we've got a bit of work to do.
"We are cracking exhausts and are having to change those every 150-200km. It's a problem we can fix but here it's difficult.
Happy Schumacher pleased with return
"We've got a handling imbalance because we are all learning about these tyres here and we've seen straight away some things we want done on the tyres which we'll have done by Jerez."
Schumacher was third fastest on both his days' running - Monday and Wednesday - with Nico Rosberg fourth quickest on Tuesday.
The seven-time world champion said: "I'm thinking we will be competitive, but whether this is a winning car straight away or not, that's another story.
"For me that's not so important - it's a long season. We need to be there and taking points from the beginning.
"I wouldn't expect to be winning right from the beginning. It wasn't something that I was aiming for and expecting to be the case. But we need to be strong enough on development."
Ferrari were fastest on all three days - with Massa setting the pace on Monday and Tuesday before handing over to Alonso for the final day.
The Brazilian's fastest lap was 0.3secs slower than Alonso's.
De la Rosa and Sauber were close to the top of the times throughout
Sauber have been the surprise package, with veteran De la Rosa second fastest on the first and third days and his Japanese team-mate Kamui Kobayashi occupying the same position on day two.
Sauber are back under the ownership of founder Peter Sauber after BMW, which had owned the team for the previous four years, decided to quit F1 following an uncompetitive season in 2009.
Button did not match the pace of team-mate Lewis Hamilton on Tuesday - but as they ran on different days no conclusions can be drawn about their relative performances.
Further down the order in terms of headline times were Renault, Williams and Toro Rosso.
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