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This problem was solved when I dectared the new point type in point_types.hpp and point_types.h exactly following the convention of the pre-existing types. In addition to this,in point_types.hpp, I had to add this new type to PCL_POINT_TYPES to make it work with kdtree and to PCL_XYZ_POINT_TYPES to make it work with ExtractIndices filter
#define PCL_POINT_TYPES \ (pcl::PointXYZ) \ (pcl::PointXYZI) \ (pcl::PointXYZRGBA) \ (pcl::PointXYZRGB) \ (pcl::PointXY) \ (pcl::InterestPoint) \ (pcl::Normal) \ (pcl::PointNormal) \ (pcl::PointXYZRGBNormal) \ (pcl::PointXYZINormal) \ (pcl::PointWithRange) \ (pcl::PointWithViewpoint) \ (pcl::MomentInvariants) \ (pcl::PrincipalRadiiRSD) \ (pcl::Boundary) \ (pcl::PrincipalCurvatures) \ (pcl::PFHSignature125) \ (pcl::FPFHSignature33) \ (pcl::VFHSignature308) \ (pcl::Narf36) \ (pcl::BorderDescription) \ (pcl::IntensityGradient) \ (pcl::Histogram<2>) \ (pcl::PointWithScale) \ (pcl::PointXYGRGBCam)
// Define all point types that include XYZ data #define PCL_XYZ_POINT_TYPES \ (pcl::PointXYZ) \ (pcl::PointXYZI) \ (pcl::PointXYZRGBA) \ (pcl::PointXYZRGB) \ (pcl::InterestPoint) \ (pcl::PointNormal) \ (pcl::PointXYZRGBNormal) \ (pcl::PointXYZINormal) \ (pcl::PointWithRange) \ (pcl::PointWithViewpoint) \ (pcl::PointWithScale) \ (pcl::PointXYGRGBCam)
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