Abstract: This invention is directed to a cassette chemical immobilization and treatment system and method for enabling the performance of various complex chemistries with minimal human intervention, near-zero dead volume, and flow-through protocols pursuant to a predetermined instruction set encoded on a multiple-address chemical treatment cassette assembly. The cassette assembly comprises a plurality of analyte sample columns ("mini-columns"), reagent wells containing pre-packaged reagents including powdered, micoencapsulated, liquid or lyophillized reagents, analyte loading funnels, alignment means for the analyte sample columns, and a machine readable instruction code set for identifying a chemical treatment protocol. The mini-columns are improved columns having high pressure interface capability to permit direct insertion of the mini-column into a high-pressure solvent line for use as a support column for HPLC analysis.