Manjusri is the Bodhisattva of Wisdom. An important aspect of the wisdom that Manjusri points to is the practical wisdom to understand the ways in which we cause harm and suffering, and to refrain from these. It can seem to us as though we have a "bodhisattva" aspect - we want to live well and to benefit beings - but that we also have a "beast" aspect - we are driven to act in unskilful ways, by tendencies that we don't fully understand. Through meditation we can explore this "black box" of the "beast of self", and we come to see that it is not the destructive force that we imagined.
Manjusri is often pictured holding the Sword of Wisdom to cut through delusion. However, if we try to wield this sword to "cut off" thoughts or feelings that we find difficult, we just end up suppressing or denying them. By sitting still and allowing them to arise, we can come to understand, accept and let go of them, and this is the functioning of the Sword of Wisdom.