When fit, he was shipped to Idaho Falls where he played two years in the advanced rookie league as a starter.
After going 0-8 with Idaho Falls, Fernandez made his debut in Eugene in 2004, again as a starter, and went 2-5 with a 5.60 ERA in 13 starts. He also made a spot start for Triple-A Portland.
But this season he was converted to reliever as the Padres hoped to take advantage of his repertoire in shorter spurts.
The first glimpse of Fernandez came in the California League where he posted three shutout innings in late May/early June. When he reappeared in Eugene, he was handed the role of closer.
With a fastball that regularly hit 95 on the radar gun, it would seem he was made to close.
"The curveball/slider is going to be the key to his success," former director of player development Tye Waller said.
Fernandez converted his first seven save opportunities but it was the eighth that was his demise. With Eugene up big, Fernandez was tagged for six runs. Although all were unearned, it affected him adversely.
"I think it was mental," one Padres' scout added. "His confidence went down."
The 6-foot-4 right-hander went on to blow six of his next seven save opportunities and was removed from the closer's role with the Emeralds.
Besides the mental aspect of the game, Fernandez became a one-trick pony, serving up the fastball and little else. That led to too many strikes being thrown and many of those were fat, giving hitters the advantage at the plate.
When Fernandez lost confidence in his secondary pitches he got tagged. Yet, he still had a .243 average against for the year.
The Venezuelan product went to the Instructional Leagues to work on the rest of his pitches this fall.
The results were sporadic as he posted a 4.61 ERA in 13.2 innings but the purpose was to get a tighter breaking ball and work on his changeup.
"High ceiling, long-range type," Bill Bryk, the Padres' minor league field coordinator, said. "He made a lot of progress in the Instructional League, along with Joel Santo and Fabian Jimenez, with their breaking ball. Very inconsistent breaking balls and actually all improved. Hopefully they can carry it into the season which is going to be a big part of them advancing.
"He just threw fastballs and didn't throw his secondary pitches. I don't care how hard you throw you have to have something else. He lost a little confidence but was good in Instructional."
At 6-foot-4, Fernandez has reportedly been overweight at times, tipping the scales above his listed 225-pound playing weight. There were rumors that he ballooned over 250 but recent reports have him slightly fitter than he was.
"It is better than it was," Grady Fuson said of his weight.
The challenge for the 21-year old prospect will be mental and physical. Dedication this off-season in controlling his weight and coming back with swagger with his secondary pitches will give him an opportunity to stick in full-season ball.
He won't turn 22 until the 2006 season ends but this will be fifth year in the Padres system. He may have upside but the clock is officially starting to tick. Putting that pressure aside will be just as important as he moves forward.