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There is a method on the fpfh estimation object to specify the indices of the source cloud points that will be used as keypoints:

PointIndicesPtr keypoints (new PointIndices);
// Compute NARF keypoints here ...

pcl::FPFHEstimation<pcl::PointXYZ, pcl::Normal, pcl::FPFHSignature33> fpfh;
fpfh.setInputCloud(sourceCloud);
fpfh.setInputNormals(normals);
fpfh.setSearchMethod(kdtree);
fpfh.setRadiusSearch(0.05);
fpfh.setIndices(keypoints);
fpfh.compute(*descriptors);
//...

This question is quite old, but I figured this might still be useful