Defects occur as self-assembled monolayers form, and the number and type of defects depend on the surface preparation and deposition solvent, among other parameters. Indirect measures to detect defects using a layer property, such as the thickness or bond vibrational frequency, are used routinely for process development but often lack sensitivity. Direct measures using an atomic probe offer a glimpse of defect structures but over a small fraction of the layer. Direct detection after reacting defects by etching or deposition is more common, and this approach has advanced our understanding of how monolayers form and has led to improved monolayers for a variety of applications. Here we show that a series of TiCl4 gas pulses reacts with defects in organosilane layers on SiO2 depositing TiO, which was measured by X-ray photoelectron spectroscopy. The defects were silanol groups and siloxane bridge bonds at the interface between the layer and the SiO2 surface and on agglomerates physisorbed to the layer. As the TiO saturation coverage or the total number of defects decreased, the incubation period in which no TiO was detected became longer. Cleaning the layer by solvent extraction to remove nonpolar agglomerates followed by an aqueous mixture of ammonium hydroxide and hydrogen peroxide, which is Standard Clean 1, a common particle removal step for silicon surfaces, produced an organosilane monolayer without agglomerates based on atomic force microscopy. After a second organosilane immersion, the monolayer density rose to 3.8 molecules/nm(2). This monolayer inhibited the deposition of TiO on the SiO2 surface for 250 pulses of TiCl4 and 200 complete TiO2 atomic layer deposition cycles using TiCl4 and water vapor, and it failed at 300 complete cycles. The Standard Clean 1 solution not only removed defects left by solvent extraction but also led to the reorganization of the organosilane layer.