diff --git a/source/AStack.cpp b/source/AStack.cpp
index db61e43..e4ed3d0 100644
--- a/source/AStack.cpp
+++ b/source/AStack.cpp
@@ -117,6 +117,11 @@ Layer* AStack::getLastLayer() const
 	return getLayer(numLayers()-1);
 }
 
+std::string AStack::projectDir(const std::string &dir) const
+{
+	return dir + "/prj/" + m_name;
+}
+
 bool AStack::save(const std::string &dir)
 {
 	return StackCreator::toFile(this, dir, m_name);
@@ -134,11 +139,12 @@ void AStack::weightsInit(double stddev)
 
 bool AStack::loadWeights(const std::string &dir)
 {
+	std::string pdir = projectDir(dir);
 	bool result = true;
 	Layer *pLayer = m_pLayers;
 	while(pLayer)
 	{
-		bool success = pLayer->weightsLoad(dir, m_name);
+		bool success = pLayer->weightsLoad(pdir, m_name);
 		if (!success)
 		{
 			pLayer->weightsInit(0.01, 0);
@@ -151,11 +157,13 @@ bool AStack::loadWeights(const std::string &dir)
 
 bool AStack::saveWeights(const std::string &dir)
 {
+	std::string pdir = projectDir(dir);
+	ensureDir(pdir);
 	bool result = true;
 	Layer *pLayer = m_pLayers;
 	while(pLayer)
 	{
-		bool success = pLayer->weightsSave(dir, m_name);
+		bool success = pLayer->weightsSave(pdir, m_name);
 		result &= success;
 		pLayer = pLayer->next;
 	}
@@ -169,8 +177,7 @@ arma::mat& AStack::trainingBatch()
 
 size_t AStack::loadTrainingBatch(const std::string &dir, bool doNormalize)
 {
-	std::string filename = dir + "/" + m_name + ".training.dat";
-	std::string path = dir + "/" + m_name + ".training.dat";
+	std::string filename = projectDir(dir) + "/" + m_name + ".training.dat";
 	bool success = m_trainingBatch.load(filename, arma::auto_detect);
 
 	if (success)
@@ -190,7 +197,9 @@ size_t AStack::loadTrainingBatch(const std::string &dir, bool doNormalize)
 
 size_t AStack::saveTrainingBatch(const std::string &dir)
 {
-	std::string filename = dir + "/" + m_name + ".training.dat";
+	std::string pdir = projectDir(dir);
+	ensureDir(pdir);
+	std::string filename = pdir + "/" + m_name + ".training.dat";
 	bool success = m_trainingBatch.save(filename, arma::arma_ascii);
 
 	if (success)
diff --git a/source/AStack.hpp b/source/AStack.hpp
index 20cd476..56fdc0d 100644
--- a/source/AStack.hpp
+++ b/source/AStack.hpp
@@ -89,7 +89,10 @@ private:
 	arma::mat m_trainingBatch;
 	size_t m_numLayers;
 	void updateNumLayers();
-	
+
+	// Every project's files live under {dir}/prj/{m_name}/, not flat at {dir}.
+	std::string projectDir(const std::string &dir) const;
+
 };
 
 #endif /* ASTACK_HPP */
diff --git a/source/StackCreator.cpp b/source/StackCreator.cpp
index dab2ef3..b44481d 100644
--- a/source/StackCreator.cpp
+++ b/source/StackCreator.cpp
@@ -14,6 +14,7 @@
 #include "StackCreator.hpp"
 #include "DeepStack.hpp"
 #include "RnnStack.hpp"
+#include "matutils.hpp"
 
 #include <string>
 #include <cassert>
@@ -77,8 +78,8 @@ AStack* StackCreator::fromJson(Json::Value& project, LayerConstructor *pLayerCon
 AStack* StackCreator::fromFile(const std::string &dir, const std::string &name, LayerConstructor *pLayerConstructor)
 {
 	std::cout << "Importing Project " << name << std::endl;
-	ifstream ifs(dir + "/" + name + string(".prj"));
-	
+	ifstream ifs(dir + "/prj/" + name + "/" + name + string(".prj"));
+
 	Json::Value project;
 	ifs >> project;
 
@@ -88,8 +89,10 @@ AStack* StackCreator::fromFile(const std::string &dir, const std::string &name,
 bool StackCreator::toFile(AStack* pStack, const std::string& dir, const std::string& name)
 {
 	std::cout << "Exporting Project " << name << std::endl;
-	ofstream ofs(dir + "/" + name + string(".prj"));
-	
+	std::string pdir = dir + "/prj/" + name;
+	Matutils::ensureDir(pdir);
+	ofstream ofs(pdir + "/" + name + string(".prj"));
+
 	Json::Value project;
 	project["stack"]["name"] = name;
 	project["stack"]["type_string"] = AStack::stackTypeStrings[pStack->type()];
diff --git a/source/matutils.hpp b/source/matutils.hpp
index cd4d02e..c7f25b6 100644
--- a/source/matutils.hpp
+++ b/source/matutils.hpp
@@ -17,9 +17,32 @@
 #include "RnnTextHelper.hpp"
 
 #include <math.h>
+#include <string>
+#include <sys/stat.h>
 
 namespace Matutils
 {
+	// Creates every missing directory component of path (like `mkdir -p`).
+	// No std::filesystem in C++11, so this is a small POSIX-only helper.
+	inline void ensureDir(const std::string &path)
+	{
+		size_t pos = 0;
+		while (pos <= path.size())
+		{
+			size_t next = path.find('/', pos);
+			if (next == std::string::npos)
+			{
+				next = path.size();
+			}
+			std::string prefix = path.substr(0, next);
+			if (!prefix.empty())
+			{
+				mkdir(prefix.c_str(), 0755);
+			}
+			pos = next + 1;
+		}
+	}
+
 	const size_t NORMALIZING_DIM = 1;
 	inline arma::mat uniform(arma::mat const & sizeMat, double stdDev=1.0, double mu=0.5)
 	{