Your kidneys are responsible for cleaning your blood and filtering out waste products. To do this, all the blood is filtered in the functional units of the kidneys call nephrons. The nephrons contain two parts, glomeruli (multiple glomerulus) and tubules. The glomerulus (one single unit) of each nephron is the first filter. Waste products of the blood are pushed out of the glomerulus through holes. Larger and important parts of the blood, red blood cells and protein, are kept inside the glomerulus and go back into circulation.
Here is a short video on how the parts of your kidneys function to keep your blood clean. He talks about the kidney, nephron and glomerulus from 3:44 - 4:48.
The system in this video is normally functioning. In MCD, the third layer of the glomerulus filter, the podocytes, have foot processes that are not shaped properly. Typically, they are very symmetrical and fit together perfectly (kind of like interlacing your fingers together tightly) so as to not allow anything important to pass through and leave our blood stream. MCD presents in foot processes that don't fit together, are too thin and are slightly elevated.
The protein is filtered out of the glomerulus, lost to the blood and voided from the body in urine. The presence of protein in the urine is called proteinuria. The picture to the right shows the holes in the glomeruli, and more specifically the slits between the foot processes of the podocytes, allowing protein to pass through along with the waste products.
References:
http://www.unckidneycenter.org/kidneyhealthlibrary/minimalchange.html
http://www.nature.com/ki/journal/v83/n3/full/ki2012412a.html#close
http://www.edren.org/pages/edreninfo/minimal-change-disease.php
