[{"rootid":"1","projects":[{"projectId":"2","proxies":[{"proxyId":"4","config":{"pipeline":[{"pipelineId":"12","desc":"pipeline"},{"pipelineId":"14","desc":"pipeline1234"}]}}]}]}]

db.collection.update({"rootid":"1"},{"$pull":{"projects.$[project].proxies.$[proxy].config.pipeline":{pipelineId:"12"}}},{arrayFilters:[{"project.projectId":"2"},{"proxy.proxyId":"4"}]})