First on the agenda is re-signing their own key free agents, like Alex Smith, Carlos Rogers and Dashon Goldson.
From there, GM Trent Baalke can begin to acquire new talent via free agency or the 2012 NFL draft. To become a consistent Super Bowl contender, the 49ers may need to add both proven stars and future stars to the roster.
With a focus on the 49ers' team needs, here are players who would have a big impact if signed by San Francisco.
Improving the anemic wide receiver corps is an absolute must for the San Francisco 49ers this offseason. If they want a proven star at the position, they should seriously consider targeting Dwayne Bowe.
Bowe has posted three seasons where he exceeded 1,000 yards receiving in his career despite playing with mediocre-at-best quarterbacks. The physical wide receiver would be the red-zone target that the 49ers so desperately need.
If Bowe is looking for greener pastures than Kansas City, San Francisco would be a fantastic fit.
Other Free Agent WRs: San Francisco may stay away from inconsistent head cases like DeSean Jackson and Stevie Johnson. As for Marques Colston, he may be a product of the New Orleans system.
The New Orleans Saints probably won't be able to re-sign Carl Nicks this offseason, giving the 49ers a chance to sign one of the best guards in the NFL.
The 6'5, 343-pound behemoth has made the past two Pro Bowls at left guard. On the 49ers, Nicks could help protect Alex Smith and open up sizable holes for Frank Gore and company.
The best fit for Nicks on the Niners would be at right guard, taking over the position from Adam Snyder.
Even if the 49ers pick up a marquee wideout in free agency, they could still use the 2012 NFL draft to grab another big-time talent at the position. Kendall Wright certainly fits the ball.
Wright has an incredible senior season at Baylor, compiling over 100 catches and 1,600 yards. His elite speed was too much for anyone in the Big 12 to handle.
The 49ers should take a long look at choosing Wright in the first round if he's available. Not only would he fill a huge need, he'd also be one of the best athletes available.
Others: If the 49ers want a bigger, more physical wideout, Mohammed Sanu of Rutgers makes a lot of sense, as would South Carolina's Alshon Jeffrey if he slips that far.
North Carolina's Dwight Jones or Arizona's Juron Criner would be great picks in the second round.
It remains unknown if Carlos Rogers will re-sign with the 49ers, though he has mentioned that he would consider a hometown discount to stay.
However, the 49ers could use cornerback help regardless of whether Rogers comes back. Stephen Gilmore may not be the fastest corner in this year's draft class, but he has great size and physicality.
If the Niners decide to use the No. 30 overall pick on a cornerback, Gilmore could be their guy.
Others: North Alabams' Janoris Jenkins and Alabama's Dre Kirkpatrick may have more upside, but they both have major red flags in the character department.
Nebraska's Alfonzo Dennard is a decent option but might be a second-round pick after a poor Senior Bowl.
If San Francisco can't reach an agreement with Ahmad Brooks, the 49ers will be looking for a pass-rusher opposite emerging star Aldon Smith.
Depending on who you ask, Courtney Upshaw could be anywhere from a top-10 pick to a late first-rounder. If he falls to the end, he could be a tremendous steal for the Niners.
Upshaw was one of the stars of Alabama's vaunted defense in 2011, recording 17 tackles for loss and 8.5 sacks. He excelled on the biggest stage, winning defensive MVP in the BCS Championship Game.
Adding Upshaw would make San Francisco's outstanding linebacker corps even more formidable.
Others: If the 49ers look for a similar player in the second round, West Virginia's Bruce Irvin or Miami's Sean Spence would be fine choices.