I used this script about three years ago for a similar purpose. It looks at an mxd and exports all of the active layers to a File GDB. It was very helpful when finishing projects and handing over working files to clients. It will probably need to be modified somewhat to meet your needs and set up as a script tool in an arcToolbox, or you can hardcode the get parameters as text lines. Again, it has been a few years since I've used it so there might be some kinks. Also, you need to create clip feature class to cover the extent of your feature classes.
# Script Name: Clip Multiple Feature Classes
# Description: Clips one or more shapefiles
# from a folder and places the clipped
# feature classes into a geodatabase.
# Created By: Insert name here.
# Date: Insert date here.
# Import ArcPy site-package and os modules
from arcpy import mapping
# Set the input workspace
#arcpy.env.workspace = arcpy.GetParameterAsText(0)
mapDocument = arcpy.GetParameterAsText(0)
# Set the clip featureclass--this should cover the extent
clipFeatures = arcpy.GetParameterAsText(1)
# Set the output workspace
outWorkspace = arcpy.GetParameterAsText(2)
# Set the XY tolerance
clusterTolerance = arcpy.GetParameterAsText(3)
fcList = 
mxd = mapping.MapDocument(mapDocument)
for df in mapping.ListDataFrames(mxd):
for lyr in mapping.ListLayers(mxd, "", df):
if lyr.dataSource not in fcList and ".gdb" in lyr.dataSource:
for fc in fcList:
featureClassname = arcpy.ValidateTableName(os.path.basename(fc), outWorkspace)
outFeatureClass = os.path.join(outWorkspace, featureClassname)
if os.path.basename(fc) != os.path.basename(clipFeatures) and not arcpy.Exists(outFeatureClass):
arcpy.AddMessage("Currently clipping the " + str(os.path.basename(fc)) + " feature...")
arcpy.Clip_analysis(fc, clipFeatures, outFeatureClass)#, clusterTolerance)
txtFile = open(os.path.dirname(outWorkspace) + os.sep + "Logfile.txt", 'w')
arcpy.env.workspace = outWorkspace
msg = "The " + os.path.basename(outWorkspace) + " contains the following features.\n\n"
i = 0
for fc in arcpy.ListFeatureClasses():
i += 1
rowCount = str(i).zfill(len(str(len(arcpy.ListFeatureClasses())))) + ". "
txtFile.write(rowCount + fc + "\n")