  We present an investigation into the effects of survey systematics such as
varying depth, point spread function (PSF) size, and extinction on the galaxy
selection and correlation in photometric, multi-epoch, wide area surveys. We
take the Canada-France-Hawaii Telescope Lensing Survey (CFHTLenS) as an
example. Variations in galaxy selection due to systematics are found to cause
density fluctuations of up to 10% for some small fraction of the area for most
galaxy redshift slices and as much as 50% for some extreme cases of faint
high-redshift samples. This results in correlations of galaxies against survey
systematics of order $\sim$1% when averaged over the survey area. We present an
empirical method for mitigating these systematic correlations from measurements
of angular correlation functions using weighted random points. These weighted
random catalogs are estimated from the observed galaxy over densities by
mapping these to survey parameters. We are able to model and mitigate the
effect of systematic correlations allowing for non-linear dependencies of
density on systematics. Applied to CFHTLenS we find that the method reduces
spurious correlations in the data by a factor two for most galaxy samples and
as much as an order of magnitude in others. Such a treatment is particularly
important for an unbiased estimation of very small correlation signals, as e.g.
from weak gravitational lensing magnification bias. We impose a criterion for
using a galaxy sample in a magnification measurement of the majority of the
systematic correlations show improvement and are less than 10% of the expected
magnification signal when combined in the galaxy cross correlation. After
correction the galaxy samples in CFHTLenS satisfy this criterion for $z_{\rm
phot}<0.9$ and will be used in a future analysis of magnification.
