SANTA CLARA, Calif. >> Jim Harbaugh wants to ensure mobile San Francisco quarterback Colin Kaepernick isn’t blatantly targeted.

So the 49ers coach has gone to the NFL for clarity about when Kaepernick is supposed to be safe before declaring himself a runner.

Kaepernick ran the read option to near perfection on the big stage against Green Bay back in January. In this scheme, quarterbacks aren’t as protected when they leave the pocket if it is clear they are runners.

“You’re hearing a lot of tough talk right now, you’re hearing some intimidating type of talk, the same thing we were hearing a couple years ago,” Harbaugh said Wednesday. “It sounds a lot like targeting a specific player. You definitely start to wonder. A man will usually tell you his bad intentions if you just listen. You know what’s being said publicly, not what’s being said privately. You hope that their intent isn’t going to be anything that’s not within the rules.”

Kaepernick ran right past the Packers in the playoffs, and through them, too.

Kaepernick’s breakout game in a breakthrough season came in his first career playoff start only two months after winning San Francisco’s starting job, carrying the 49ers to a 45-31 divisional-round victory in which he ran for a pair of touchdowns and threw for two more.

He set a quarterback playoff record in the process with 181 yards rushing in the win that sent San Francisco to a second straight NFC title game.

Kaepernick said he can’t concern himself with the defense’s motivations

“I’m not worried about that,” he said. “It’s football, you’re going to get hit.”

Green Bay had no answer for the Niners’ spot-on read option. Coach Mike McCarthy said the biggest problem for the Packers was getting Kaepernick when he scrambled out of the pocket.

When asked whether he was surprised at just how well everything went, Kaepernick responded: “You’re supposed to go out and perform as players. That’s what you get paid to do. You can only line 11 people up so many ways, so we’ve seen a lot of different looks.”

Linebacker Clay Matthews insists the Packers will be better prepared come Sunday’s season opener at Candlestick Park when they try again to slow down — and stop — Kaepernick.

“For the most part we had the entire offseason to focus on this,” Matthews said Wednesday. “You look at the progression of the league and specifically quarterbacks, Kaepernick, you look at Washington, Seattle, there are quarterbacks around the league that present problems not only with their arms but with their legs, too. Whether that’s in the pistol or the read-option offense, they’re becoming more and more difficult to contest. We had an entire offseason to focus on last year’s loss, having time to kind of figure out a way to defend that. We obviously like to think we’re better prepared to defend that type of offense and what he brings to the table.”

Harbaugh plans to speak to the officials before the game about what the coach calls a “gray area” in the rules. He doesn’t expect to hear back from the league before the game.

“Those are the conversations right now,” Harbaugh said. “I haven’t gotten the final clarification on what it’s going to be.”

San Francisco had 579 total yards with 323 on the ground in the playoff win, scoring its third-most points in the franchise’s storied playoff history.

“I can assure you they’re trying everything they possibly can to try and stop Kaepernick and the rest of this offense,” said 49ers tight end Vernon Davis, who has a touchdown catch in each of his four regular-season games against Green Bay. “The read option, it’s not a joke, it’s nothing to play with. You have to really be prepared, you have to do your due diligence on the read option before you can defend it. Especially when you have a guy like Kaepernick who can run really well, he’s fast and makes the correct decisions. He’s really disciplined when it comes to that phase, and they’re definitely going to have to be prepared, and I know they will.”

When reminded of how thoroughly his Packers were dominated by Kaepernick in the quarterback’s record-setting day, Green Bay coach Mike McCarthy made a point that this is a new season.

“That’s well stated, I think anybody would be motivated when it’s directed at you like that. But the reality is, it is a new year, this is a different game, and we’re prepared for a totally different outcome,” McCarthy said upon hearing Kaepernick’s stats once more. “He had a heck of a night last year.”

Notes: LB Patrick Willis, nursing a broken right hand, is expected to play Sunday. He hopes to be brace-free. “I’m going through some different contraptions, not sure what I’m going to end up with on game day,” he said. “Hopefully, it will be nothing.” … Matthews said he might try to talk to former 49ers QB Scott Tolzien, now in Green Bay. “Maybe I should set aside an hour or so to pick his brain,” Matthews said. … When Harbaugh was asked whether he had spoken with LB Aldon Smith regarding a lawsuit naming him by a man who said he was shot during a party at Smith’s house in June 2012, the coach said, “The team is handling it.” Smith said the lawsuit was no surprise but he declined to discuss it specifically.