A method of purifying extracellular vesicles in a sample comprising extracellular vesicles and molecules that are not bound to the extracellular vesicles, the method comprising: (a) providing a mixed mode resin composition comprising a first resin having pores with a pore size that traps unbound molecules having a size less than or equal to 1,000,000 Da in its pores by at least by a size exclusion mechanism, wherein the first resin comprises a first bead comprising (i) a porous core comprising a matrix material and at least one affinity ligand, (ii) a porous shell, and (iii) optionally at least one second affinity ligand coated on the exterior surface of the bead; and a second resin comprising at least one affinity ligand, wherein the second resin binds at least a portion of the unbound molecules, wherein the second resin comprises a second bead comprising a matrix material and at least one ligand coated on an exterior surface of the second bead that has an affinity for at least one unbound molecule in the sample; (b) contacting the sample with the mixed mode resin composition for a time sufficient to trap at least a portion of the unbound molecules having a size less than or equal to 1,000,000 Da in the first resin from the sample; and (c) separating the sample from the mixed mode resin composition after the contacting in (b) and obtaining a sample containing extracellular vesicles at a higher concentration than prior to step (b). (a) providing a mixed mode resin composition comprising a first resin having pores with a pore size that traps unbound molecules having a size less than or equal to 1,000,000 Da in its pores by at least by a size exclusion mechanism, wherein the first resin comprises a first bead comprising (i) a porous core comprising a matrix material and at least one affinity ligand, (ii) a porous shell, and (iii) optionally at least one second affinity ligand coated on the exterior surface of the bead; and a second resin comprising at least one affinity ligand, wherein the second resin binds at least a portion of the unbound molecules, wherein the second resin comprises a second bead comprising a matrix material and at least one ligand coated on an exterior surface of the second bead that has an affinity for at least one unbound molecule in the sample; a first resin having pores with a pore size that traps unbound molecules having a size less than or equal to 1,000,000 Da in its pores by at least by a size exclusion mechanism, wherein the first resin comprises a first bead comprising (i) a porous core comprising a matrix material and at least one affinity ligand, (ii) a porous shell, and (iii) optionally at least one second affinity ligand coated on the exterior surface of the bead; and a second resin comprising at least one affinity ligand, wherein the second resin binds at least a portion of the unbound molecules, wherein the second resin comprises a second bead comprising a matrix material and at least one ligand coated on an exterior surface of the second bead that has an affinity for at least one unbound molecule in the sample; (b) contacting the sample with the mixed mode resin composition for a time sufficient to trap at least a portion of the unbound molecules having a size less than or equal to 1,000,000 Da in the first resin from the sample; and (c) separating the sample from the mixed mode resin composition after the contacting in (b) and obtaining a sample containing extracellular vesicles at a higher concentration than prior to step (b).