In this article, different manifold reduction techniques are implemented for the post-processing of Particle Image Velocimetry (PIV) images from a Spark Ignition Direct Injection (SIDI) engine. The methods are proposed to help make a more objective comparison between Reynolds-averaged Navier-Stokes (RANS) simulations and PIV experiments when Cycle-to-Cycle Variations (CCV) are present in the flow field. The two different methods used here are based on Singular Value Decomposition (SVD) principles where Proper Orthogonal Decomposition (POD) and Kernel Principal Component Analysis (KPCA) are used for representing linear and non-linear manifold reduction techniques. To the authorsā best knowledge, this is the first time a non-linear manifold reduction technique, such as KPCA, has ever been used in the study of in-cylinder flow fields. Both qualitative and quantitative studies are given to show the capability of each method in validating the simulation and incorporating CCV for each engine cycle. Traditional Relevance Index (RI) and two other previously developed novel indexes: the Weighted Relevance Index (WRI) and the Weighted Magnitude Index (WMI), are used for the quantitative study. The results indicate that both POD and KPCA show improvements in capturing the main flow field features compared to ensemble-averaged PIV experimental data and single cycle experimental flow fields while capturing CCV. Both methods present similar quantitative accuracy when using the three indexes. However, challenges were highlighted in the POD method for the selection of the number of POD modes needed for a representative reconstruction. When the flow field region presents a Gaussian distribution, the KPCA method is seen to provide a more objective numerical process as the reconstructed flow field will see convergence with an increasing number of modes due to its usage of Gaussian properties. No additional criterion is needed to determine how to reconstruct the main flow field feature. Using KPCA can, therefore, reduce the amount of analysis needed in the process of extracting the main flow field while incorporating CCV.