diff --git a/matlab/EKF_replay/Filter/PlotData.m b/matlab/EKF_replay/Filter/PlotData.m
index c9bf87b7f6..3d3bf7c673 100644
--- a/matlab/EKF_replay/Filter/PlotData.m
+++ b/matlab/EKF_replay/Filter/PlotData.m
@@ -1,8 +1,5 @@
-function PlotData(output)
+function PlotData(output,folder,runIdentifier)
 rad2deg = 180/pi;
-runIdentifier = ' : EKF replay ';
-folder = strcat('../OutputPlots');
-
 if ~exist(folder,'dir')
     mkdir(folder);
 end
diff --git a/matlab/EKF_replay/Filter/replay_apm_data.m b/matlab/EKF_replay/Filter/replay_apm_data.m
index 2175db730d..7165cfc232 100644
--- a/matlab/EKF_replay/Filter/replay_apm_data.m
+++ b/matlab/EKF_replay/Filter/replay_apm_data.m
@@ -32,12 +32,14 @@ run('SetParameterDefaults.m');
 % run the filter replay 
 output = RunFilter(param,imu_data,mag_data,baro_data,gps_data,rng_data,flow_data,viso_data);
 
-% genrate and save output plots
-PlotData(output);
+% generate and save output plots
+runIdentifier = ' : APM data replay ';
+folder = strcat('../OutputPlots/APM');
+PlotData(output,folder,runIdentifier);
 
 % save output data
-folder = '../OutputData';
-fileName = '../OutputData/ekf_replay_output.mat';
+folder = '../OutputData/APM';
+fileName = '../OutputData/APM/ekf_replay_output.mat';
 if ~exist(folder,'dir')
     mkdir(folder);
 end
diff --git a/matlab/EKF_replay/Filter/replay_px4_data.m b/matlab/EKF_replay/Filter/replay_px4_data.m
index 36a0593a71..c542a773fd 100644
--- a/matlab/EKF_replay/Filter/replay_px4_data.m
+++ b/matlab/EKF_replay/Filter/replay_px4_data.m
@@ -17,11 +17,13 @@ run('SetParameterDefaults.m');
 output = RunFilter(param,imu_data,mag_data,baro_data,gps_data);
 
 % generate and save output plots
-PlotData(output);
+runIdentifier = ' : PX4 data replay ';
+folder = strcat('../OutputPlots/PX4');
+PlotData(output,folder,runIdentifier);
 
 % save output data
-folder = '../OutputData';
-fileName = '../OutputData/ekf_replay_output.mat';
+folder = '../OutputData/PX4';
+fileName = '../OutputData/PX4/ekf_replay_output.mat';
 if ~exist(folder,'dir')
     mkdir(folder);
 end