This is a phrase used in baseball to describe what happens after a home run or other big hit by the offense when other players are on base. By hitting a home run or making another big hit, a player can clear the bases of his teammates, sending all of them home. Each runner who makes it home scores a run for the offense and adds a "run batted in" or RBI for the hitter. A defensive player would not want to clear the bases, as this would mean his efforts resulted in runs for the opposition. Clearing the bases is positive-every offensive player wants to clear the bases when he is at bat.
This phrase comes from the act of runners leaving the field after a home run or a big hit. After crossing home plate and recording a run, a player will go back into the dugout. The player who made the hit will have "cleared" the bases. The most extreme example of clearing the bases is a grand slam. A grand slam occurs when the bases are loaded, which means there is a runner at every base, and the hitter hits a home run, scoring runs for everyone on base and himself. Since a grand slam is not a common occurrence, it is considered one of the greatest types of hits in baseball.