The present invention creates a biologically protected or enhanced space in vivo in a mammal to allow the mammals immune system and/or other biological processes to function properly in order to treat autoimmune diseases. In particular, the biologically protected/enhanced space allows biological processes to occur that can therapeutically treat Type I diabetes. The biologically enhanced/protected space can also be used to promote growth of specific cells such as insulin producing islet cells of the pancreas. Microfluidic devices can also be used to remove soluble TNF receptors and autoreactive T Cells in treating autoimmune diseases. Additionally, microfluidic devices can be used to remove blood glucose, soluble insulin receptors and insulin-like growth factor (IGF) from blood in the treatment of adult onset (Type II) diabetes.