Process integration techniques are disclosed that use a carbon fill layer during formation of self-aligned structures. A carbon layer may be placed over an etch stop layer. A cap layer may be provided over the carbon layer. The carbon layer may fill a high aspect ratio structure formed on the substrate. The carbon layer may be removed from a substrate in a highly selective removal technique in a manner that does not damage underlying layers. The carbon layer may fill a self-aligned contact region that is provided for a self-aligned contact process flow. A tone inversion mask may be used to protect multiple self-aligned contact regions. With the blocking mask in place, the carbon layer may be removed from regions that are not the self-aligned contact region. After removal of the blocking mask, the carbon layer which fills the self-aligned contacts may then be removed.