I assume you mean parts of a cell that are too small to be seen with a basic light microscope. No parts of a cell can be seen with the naked eye. The subunits of cells are called organelles. Three organelles that cannot be readily seen with a light microscope are endoplasmic reticulum, ribosomes, and Golgi apparatus. The endoplasmic reticulum helps fold and process proteins. The ribosomes are located on the rough endoplasmic reticulum and are the sites of protein synthesis. The Golgi apparatus also modifies proteins for use. Some organelles that are too small to be seen can be made visible through the use of special stains which are dyes that color certain parts of the cell to make them easier to see.