Nodules occur when clogged, swollen pores endure further irritation and grow larger. Unlike pustules and papules, nodules are deeper underneath the skin.Because nodules are so deep within the skin, you can’t typically treat them at home. Prescription medication is necessary to help clear these up.Your doctor or dermatologist will likely prescribe the oral medication isotretinoin (Sotret). This is made from a form of vitamin A and is taken daily for four to six months. It can treat and prevent nodules by decreasing oil gland size within the pores.