A method for performing a calibration routine in a three-dimensional modeling machine, that builds-up three-dimensional objects as directed by a controller by depositing modeling material with first and second deposition devices (38, 40) onto a substrate mounted on a platform, the method comprising: generating a material build profile, wherein the material build profile represents a three-dimensional structure at defined locations, comprising building a first pad on the platform using the first deposition device; determining a relative position of the material build profile, comprising: sensing a top surface of the first pad at a first defined X,Y location; sensing a top surface of the substrate mounted on the platform at a second defined X,Y location; and using a combination of the sensed positions to calculate an actual height of the first pad; identifying an expected build profile; comparing the relative position of the material build profile to the expected build profile to determine a tip-to-substrate offset, comprising determining a difference between the actual height of the first pad and an expected height of the first pad to determine the tip-to-substrate offset; building a second pad on the platform using the second deposition device; sensing a top surface of the second pad at a third defined X,Y location; and determining a difference between the top surfaces corresponding to the sensing of the first pad and the sensing of the second pad to determine a relative tip-to-tip offset along a Z-axis between the first and second deposition devices; and positioning the first deposition device based upon the tip-to-substrate offset. generating a material build profile, wherein the material build profile represents a three-dimensional structure at defined locations, comprising building a first pad on the platform using the first deposition device; determining a relative position of the material build profile, comprising: sensing a top surface of the first pad at a first defined X,Y location; sensing a top surface of the substrate mounted on the platform at a second defined X,Y location; and using a combination of the sensed positions to calculate an actual height of the first pad; sensing a top surface of the first pad at a first defined X,Y location; sensing a top surface of the substrate mounted on the platform at a second defined X,Y location; and using a combination of the sensed positions to calculate an actual height of the first pad; identifying an expected build profile; comparing the relative position of the material build profile to the expected build profile to determine a tip-to-substrate offset, comprising determining a difference between the actual height of the first pad and an expected height of the first pad to determine the tip-to-substrate offset; building a second pad on the platform using the second deposition device; sensing a top surface of the second pad at a third defined X,Y location; and determining a difference between the top surfaces corresponding to the sensing of the first pad and the sensing of the second pad to determine a relative tip-to-tip offset along a Z-axis between the first and second deposition devices; and positioning the first deposition device based upon the tip-to-substrate offset.