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I have two shape files, with the same coordinate system (File 1 and File 2).
I have defined the Projection/Coordinate System of File 2 in ArcGIS using ArcToolbox using the Data Management Tools/Projections and Transformations/Define Projection.

For selecting the coordinate system. I have used the import button and have it use the same coordinate system of file 2.

Everything seems right the current coordinate system of both files is the same, but the files don’t align /overlap. What is wrong with these files? The only strange thing that I find is the Units that in both cases are “Unknown Units”.

The data source box of both files is the same :

Data Type:  Shapefile Feature Class 
Shapefile:  C:\SIG\Cartografia\Cartas_uso_do_solo\CLC06_PT\CLC06_PT.shp
Geometry Type:  Polygon
Coordinates have Z values:  No 
Coordinates have measures:  No 

Projected Coordinate System:    ETRS_1989_Portugal_TM06
Projection: Transverse_Mercator
False_Easting:  0.00000000
False_Northing: 0.00000000
Central_Meridian:   -8.13310833
Scale_Factor:   1.00000000
Latitude_Of_Origin: 39.66825833
Linear Unit:    Meter

Geographic Coordinate System:   GCS_ETRS_1989
Datum:  D_ETRS_1989
Prime Meridian:     Greenwich
Angular Unit:   Degree
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    You state that you defined the CRS of the files. Did the files not have any CRS originally? If so, they might not necessarily have been in the same CRS to start with and there is a big difference between defining the CRS and actually transforming a projection. – MappaGnosis Sep 15 '14 at 13:20
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Yes, positional error (i.e. error in the x-y coordinates of features), means that features will not necessarily line up perfectly regardless of whether they are in the same coordinate system. Each measured point will have some level of positional error which will depend on many factors including the methods by which the data are collected, e.g. using a GPS, surveying equipment, or digitized from a satellite image.

While, this answers the question you posed, it is not necessarily the reason that you are finding your specific data does not overlap. As a commenter points out, if your data are not originally in the same CRS and you have not performed a re-projection, or if the CRS was not originally defined, they will not line up correctly.

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  • Even though all of these are valid reasons for data not aligning properly, it will still be on the scale of a few meters at most. If they are off more than that it is way more likely, as @MappaGnosis says, that the files weren't in the same coordinate system to begin with. – Martin Sep 15 '14 at 13:25
  • If the geographic data stored in the .prj file is the same in both files, I can be sure that the problem can only be positional error? – Manuel Almeida Sep 15 '14 at 13:27
  • @ManuelAlmeida, No, I think that in your specific case, there is more at play here than simply positional error. It is true however that because of positional error, two overlapping features are likely to experience some degree of offset. I think MappaGnosis has a good point specific to your case in their comment above. – WhiteboxDev Sep 15 '14 at 13:29
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    @ManuelAlmeida You should have a look at this question, since the issue of shapefiles not overlapping due to coordinate system confusion is one of the most common errors while working with spatial data. – Martin Sep 15 '14 at 13:32

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